Merge branch 'release-1.29.0' into release

ugeneunipro · Dec 29, 2017 · dbf0992 · dbf0992
2 parents 85a50bc + a240beb
commit dbf0992
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -5,18 +5,18 @@
 #   * add Qt5_DIR variable to File->Settings->Build,Execution,Deployment->CMake pointing to valid QT dir.
 #   * add UGENE_TRANSLATION_FILE environment variable to the RUN configuration and point it to *.qm file produced by qmake build
 
-cmake_minimum_required(VERSION 3.4)
+cmake_minimum_required(VERSION 3.9)
 project(ugene)
 
 #set(CMAKE_VERBOSE_MAKEFILE ON)
 
-set(UGENE_VERSION 1.25.0-dev)
+set(UGENE_VERSION 1.29.0-dev)
 set(UGENE_VER_MAJOR 1)
-set(UGENE_VER_MINOR 25)
+set(UGENE_VER_MINOR 29)
 set(UGENE_VER_PATCH 0)
 
-set(UGENE_MIN_VERSION_SQLITE 1.13.0)
-set(UGENE_MIN_VERSION_MYSQL 1.16.0)
+set(UGENE_MIN_VERSION_SQLITE 1.25.0)
+set(UGENE_MIN_VERSION_MYSQL 1.25.0)
 
 add_definitions(
         -DUGENE_VERSION=${UGENE_VERSION}

diff --git a/installer/_common_data/README b/installer/_common_data/README
@@ -32,7 +32,7 @@ UGENE main features:
 
 UGENE is licensed via GPLv2.
 
-Please, visit http://ugene.unipro.ru for more details.
+Please, visit http://ugene.net for more details.
 
 
 -----------------------------
@@ -67,7 +67,7 @@ There is man page available for command-line version:
 man man1/ugene.1.gz
 
 For complete user documentation visit:
-http://ugene.unipro.ru/manual
+http://ugene.net/manual
 
 
 -------------------

diff --git a/installer/linux/ubuntu/debian/control b/installer/linux/ubuntu/debian/control
@@ -5,7 +5,7 @@ Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 XSBC-Original-Maintainer: Ivan Efremov <iefremov@unipro.ru>
 Build-Depends: qt5-default, qttools5-dev-tools, libqt5webkit5-dev, libqt5opengl5-dev, libqt5sql5-mysql, qtscript5-dev, libqt5svg5-dev, zlib1g-dev, libprocps4-dev, debhelper (>=5.0.38)
 Standards-Version: 3.9.3
-Homepage: http://ugene.unipro.ru
+Homepage: http://ugene.net
 
 Package: ugene
 Architecture: any

diff --git a/installer/linux/ubuntu/debian/copyright b/installer/linux/ubuntu/debian/copyright
@@ -1,7 +1,7 @@
 This package was debianized by Ivan Efremov <iefremov@unipro.ru> on
 Mon, 26 Jan 2009 19:18:51 +0600
 
-It was downloaded from: http://ugene.unipro.ru/download.html
+It was downloaded from: http://ugene.net/download.html
 
 Modifications to the original source package:
     The following directories have been removed:

diff --git a/installer/linux/ubuntu/debian/watch b/installer/linux/ubuntu/debian/watch
@@ -1,4 +1,4 @@
 version=3
 opts=dversionmangle=s/\+repack// \
-http://ugene.unipro.ru/ugene_get_latest_source.html \
+http://ugene.net/ugene_get_latest_source.html \
   downloads/ugene-([\d.]*)\.tar\.gz debian uupdate
diff --git a/src/corelibs/U2Algorithm/src/util_gpu/opencl/BinaryFind.cl b/src/corelibs/U2Algorithm/src/util_gpu/opencl/BinaryFind.cl
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -78,9 +78,9 @@ __kernel void
             mid = low + (high - low) / 2;
             curValue = haystack[mid] & filter;
         }
-        
+
         if (curValue == needle) {
-            for(firstOccurrenceOffset = mid; 
+            for(firstOccurrenceOffset = mid;
                 firstOccurrenceOffset >= 0 && (haystack[firstOccurrenceOffset] & filter) == needle;
                 firstOccurrenceOffset--) {};
 

diff --git a/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.cpp b/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.h b/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.h
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Algorithm/src/util_msa_distance/BuiltInDistanceAlgorithms.cpp b/src/corelibs/U2Algorithm/src/util_msa_distance/BuiltInDistanceAlgorithms.cpp
@@ -24,7 +24,7 @@
 namespace U2 {
 
     const QString BuiltInDistanceAlgorithms::HAMMING_ALGO("Hamming dissimilarity");
-	const QString BuiltInDistanceAlgorithms::SIMILARITY_ALGO("Identity");
+    const QString BuiltInDistanceAlgorithms::SIMILARITY_ALGO("Similarity");
     const QString BuiltInDistanceAlgorithms::HAMMING_REVCOMPL_ALGO("Hamming reverse-complement");
 
 }//namespace
diff --git a/src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorScheme.cpp b/src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorScheme.cpp
@@ -306,7 +306,19 @@ void addUgeneSangerNucleotide(QVector<QColor> &colorsPerChar) {
     SET_C('G', "#DADADA");
     SET_C('T', "#FE7276");
     SET_C('N', Qt::magenta);
-    SET_C(U2Msa::GAP_CHAR, "#FF9700");
+    SET_C('M', Qt::magenta);
+    SET_C('R', Qt::magenta);
+    SET_C('W', Qt::magenta);
+    SET_C('S', Qt::magenta);
+    SET_C('Y', Qt::magenta);
+    SET_C('K', Qt::magenta);
+    SET_C('V', Qt::magenta);
+    SET_C('H', Qt::magenta);
+    SET_C('D', Qt::magenta);
+    SET_C('B', Qt::magenta);
+    SET_C('X', Qt::magenta);
+
+    colorsPerChar[U2Msa::GAP_CHAR] = "#FF9700";
 }
 
 void addZappoAmino(QVector<QColor> &colorsPerChar) {

diff --git a/src/corelibs/U2Algorithm/transl/english.ts b/src/corelibs/U2Algorithm/transl/english.ts
@@ -363,7 +363,7 @@ For every column selects the most rare symbol in the whole alignment with percen
     <message>
         <location filename="../src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.cpp" line="203"/>
         <source>Simple extended</source>
-        <translation type="unfinished"></translation>
+        <translation></translation>
     </message>
 </context>
 <context>
@@ -388,69 +388,69 @@ For every column selects the most rare symbol in the whole alignment with percen
 <context>
     <name>U2::MsaColorSchemeRegistry</name>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="533"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="545"/>
         <source>No colors</source>
         <translation>No colors</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="541"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="553"/>
         <source>UGENE Sanger</source>
         <translation type="unfinished"></translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="545"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="557"/>
         <source>Jalview</source>
         <translation>Jalview</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="547"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="585"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="597"/>
         <source>Percentage Identity</source>
         <translation>Percentage Identity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="548"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="586"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="560"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="598"/>
         <source>Percentage Identity (gray)</source>
         <translation>Percentage Identity (gray)</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="571"/>
         <source>Zappo</source>
         <translation>Zappo</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="563"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="575"/>
         <source>Tailor</source>
         <translation>Tailor</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="567"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="579"/>
         <source>Hydrophobicity</source>
         <translation>Hydrophobicity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="571"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="583"/>
         <source>Helix propensity</source>
         <translation>Helix propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="575"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="587"/>
         <source>Strand propensity</source>
         <translation>Strand propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="579"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="591"/>
         <source>Turn propensity</source>
         <translation>Turn propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="583"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="595"/>
         <source>Buried index</source>
         <translation>Buried index</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="588"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="600"/>
         <source>Clustal X</source>
         <translation>Clustal X</translation>
     </message>

diff --git a/src/corelibs/U2Algorithm/transl/russian.ts b/src/corelibs/U2Algorithm/transl/russian.ts
@@ -390,69 +390,69 @@ For every column selects the most rare symbol in the whole alignment with percen
 <context>
     <name>U2::MsaColorSchemeRegistry</name>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="533"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="545"/>
         <source>No colors</source>
         <translation>Без цвета</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="541"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="553"/>
         <source>UGENE Sanger</source>
         <translation type="unfinished"></translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="545"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="557"/>
         <source>Jalview</source>
         <translation>Раскраска Jalview</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="547"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="585"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="597"/>
         <source>Percentage Identity</source>
         <translation>По процентному соотношению</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="548"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="586"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="560"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="598"/>
         <source>Percentage Identity (gray)</source>
         <translation>По процентному соотношению (серый)</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="571"/>
         <source>Zappo</source>
         <translation>Zappo</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="563"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="575"/>
         <source>Tailor</source>
         <translation>Tailor</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="567"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="579"/>
         <source>Hydrophobicity</source>
         <translation>Гидрофобность</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="571"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="583"/>
         <source>Helix propensity</source>
         <translation>Склонность к спиральности</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="575"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="587"/>
         <source>Strand propensity</source>
         <translation>Склонность к линейности</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="579"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="591"/>
         <source>Turn propensity</source>
         <translation>Склонность к сворачиванию</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="583"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="595"/>
         <source>Buried index</source>
         <translation>Индекс</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="588"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="600"/>
         <source>Clustal X</source>
         <translation>Clustal X</translation>
     </message>

diff --git a/src/corelibs/U2Core/src/datatype/DNAChromatogram.cpp b/src/corelibs/U2Core/src/datatype/DNAChromatogram.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/U2Mca.cpp b/src/corelibs/U2Core/src/datatype/U2Mca.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/U2Mca.h b/src/corelibs/U2Core/src/datatype/U2Mca.h
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/U2Msa.cpp b/src/corelibs/U2Core/src/datatype/U2Msa.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/msa/MaStateCheck.cpp b/src/corelibs/U2Core/src/datatype/msa/MaStateCheck.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/msa/MaStateCheck.h b/src/corelibs/U2Core/src/datatype/msa/MaStateCheck.h
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/msa/MultipleAlignment.cpp b/src/corelibs/U2Core/src/datatype/msa/MultipleAlignment.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/msa/MultipleAlignment.h b/src/corelibs/U2Core/src/datatype/msa/MultipleAlignment.h
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License

diff --git a/src/corelibs/U2Core/src/datatype/msa/MultipleAlignmentRow.cpp b/src/corelibs/U2Core/src/datatype/msa/MultipleAlignmentRow.cpp
@@ -1,7 +1,7 @@
 /**
  * UGENE - Integrated Bioinformatics Tools.
  * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
- * http://ugene.unipro.ru
+ * http://ugene.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License