Merge branch 'release-1.28.1' into release

ugeneunipro · Nov 20, 2017 · 85a50bc · 85a50bc
2 parents e7b86c5 + cda6990
commit 85a50bc
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Showing 96 changed files with 5,466 additions and 3,026 deletions.
diff --git a/data/cmdline/align-to-reference.uwl b/data/cmdline/align-to-reference.uwl
@@ -35,8 +35,8 @@ workflow "Trim and map Sanger reads"{
     }
 
     .actor-bindings {
-        read-sequence.out-sequence->SequenceQualityTrim.in-sequence
         SequenceQualityTrim.out-sequence->align-to-reference.in-sequence
+        read-sequence.out-sequence->SequenceQualityTrim.in-sequence
     }
 
     read-sequence.sequence->SequenceQualityTrim.in-sequence.sequence
@@ -65,24 +65,27 @@ workflow "Trim and map Sanger reads"{
             align-to-reference.result-url {
                 alias:result-url;
             }
+            align-to-reference.row-naming-policy {
+                alias:row-naming-policy;
+            }
         }
         visual {
             SequenceQualityTrim {
-                pos:"-705 -555";
+                pos:"-675 -525";
                 style:ext;
                 bg-color-ext:"0 128 128 64";
                 in-sequence.angle:180;
                 out-sequence.angle:360;
             }
             align-to-reference {
-                pos:"-405 -540";
+                pos:"-375 -510";
                 style:ext;
                 bg-color-ext:"0 128 128 64";
                 in-sequence.angle:180;
                 out.angle:360;
             }
             read-sequence {
-                pos:"-960 -540";
+                pos:"-930 -510";
                 style:ext;
                 bg-color-ext:"0 128 128 64";
                 out-sequence.angle:360;

diff --git a/data/workflow_samples/Sanger sequencing/trim-and-align.uwl b/data/workflow_samples/Sanger sequencing/trim-and-align.uwl
@@ -93,7 +93,7 @@ workflow "Trim and map Sanger reads"{
         wizard {
             help-page-id:16122701;
 	    auto-run: true;
-            name:"Trim and Map Sanger Reads";
+            name:"Map Sanger Reads to Reference";
             page {
                 id:1;
                 next:2;
@@ -121,14 +121,16 @@ workflow "Trim and map Sanger reads"{
             page {
                 id:3;
                 next:4;
-                title:"Trimming and Filtering";
+                title:"Mapping Settings";
                 parameters-area {
                     group {
                         title:"Settings";
-                        label-size:120;
+                        label-size:220;
                         SequenceQualityTrim.qual-id {
                         }
-                        SequenceQualityTrim.len-id {
+                        align-to-reference.identity {
+                        }
+                        align-to-reference.row-naming-policy {
                         }
                     }
                 }

diff --git a/src/corelibs/U2Algorithm/src/misc/FindAlgorithm.cpp b/src/corelibs/U2Algorithm/src/misc/FindAlgorithm.cpp
@@ -831,7 +831,7 @@ void FindAlgorithm::find(
 
     bool insDel = (patternSettings == FindAlgorithmPatternSettings_InsDel);
 
-    if (patternSettings == FindAlgorithmPatternSettings_Exact && sequenceAlphabet != NULL) {
+    if (patternSettings == FindAlgorithmPatternSettings_Exact && sequenceAlphabet != NULL && aminoTT == NULL) {
         // exact search -> do not run any search if pattern has illegal symbols
         if (!U2AlphabetUtils::matches(sequenceAlphabet, pattern, patternLen)) {
             return;

diff --git a/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.h b/src/corelibs/U2Algorithm/src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.h
@@ -116,6 +116,7 @@ class MaConsensusAlgorithmSimpleExtended : public MSAConsensusAlgorithm {
 Q_DECLARE_OPERATORS_FOR_FLAGS(MaConsensusAlgorithmSimpleExtended::Characters)
 
 class MaConsensusAlgorithmFactorySimpleExtended : public MSAConsensusAlgorithmFactory {
+    Q_OBJECT
 public:
     MaConsensusAlgorithmFactorySimpleExtended(QObject *parent = NULL);
 

diff --git a/src/corelibs/U2Algorithm/transl/english.ts b/src/corelibs/U2Algorithm/transl/english.ts
@@ -53,7 +53,7 @@
         <translation>Some errors occurs in library: %1</translation>
     </message>
     <message>
-        <location filename="../src/util_msa_consensus/MSAConsensusUtils.cpp" line="107"/>
+        <location filename="../src/util_msa_consensus/MSAConsensusUtils.cpp" line="108"/>
         <source>Gaps:</source>
         <translation>Gaps:</translation>
     </message>
@@ -181,7 +181,7 @@
 <context>
     <name>U2::BestPositionFindTask</name>
     <message>
-        <location filename="../src/msa_alignment/SimpleAddingToAlignment.cpp" line="108"/>
+        <location filename="../src/msa_alignment/SimpleAddingToAlignment.cpp" line="120"/>
         <source>Best position find task</source>
         <translation>Best position find task</translation>
     </message>
@@ -210,7 +210,7 @@
 <context>
     <name>U2::DnaAssemblyToReferenceTask</name>
     <message>
-        <location filename="../src/registry/DnaAssemblyTask.cpp" line="30"/>
+        <location filename="../src/registry/DnaAssemblyTask.cpp" line="34"/>
         <source>Align short reads</source>
         <translation>Align short reads</translation>
     </message>
@@ -234,12 +234,12 @@
 <context>
     <name>U2::LoadPatternsFileTask</name>
     <message>
-        <location filename="../src/misc/FindAlgorithmTask.cpp" line="107"/>
+        <location filename="../src/misc/FindAlgorithmTask.cpp" line="108"/>
         <source>Load pattern from file</source>
         <translation>Load pattern from file</translation>
     </message>
     <message>
-        <location filename="../src/misc/FindAlgorithmTask.cpp" line="128"/>
+        <location filename="../src/misc/FindAlgorithmTask.cpp" line="129"/>
         <source>Detecting format error for file %1</source>
         <translation>Detecting format error for file %1</translation>
     </message>
@@ -273,14 +273,14 @@
 <context>
     <name>U2::MSAConsensusAlgorithmFactoryLevitsky</name>
     <message>
-        <location filename="../src/util_msa_consensus/MSAConsensusAlgorithmLevitsky.cpp" line="38"/>
+        <location filename="../src/util_msa_consensus/MSAConsensusAlgorithmLevitsky.cpp" line="36"/>
         <source>The algorithm proposed by Victor Levitsky to work with DNA alignments.
 Collects global alignment frequency for every symbol using extended (15 symbols) DNA alphabet first.
 For every column selects the most rare symbol in the whole alignment with percentage in the column greater or equals to the threshold value.</source>
         <translation></translation>
     </message>
     <message>
-        <location filename="../src/util_msa_consensus/MSAConsensusAlgorithmLevitsky.cpp" line="46"/>
+        <location filename="../src/util_msa_consensus/MSAConsensusAlgorithmLevitsky.cpp" line="44"/>
         <source>Levitsky</source>
         <translation></translation>
     </message>
@@ -353,6 +353,19 @@ For every column selects the most rare symbol in the whole alignment with percen
         <translation>An unexpected error has occurred during running the Hamming reverse-complement algorithm.</translation>
     </message>
 </context>
+<context>
+    <name>U2::MaConsensusAlgorithmFactorySimpleExtended</name>
+    <message>
+        <location filename="../src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.cpp" line="198"/>
+        <source>The algorithm selects the best character from the extended DNA alphabet. Only bases with frequences which are greater than a threshold value are taken into account.</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="../src/util_msa_consensus/MaConsensusAlgorithmSimpleExtended.cpp" line="203"/>
+        <source>Simple extended</source>
+        <translation type="unfinished"></translation>
+    </message>
+</context>
 <context>
     <name>U2::MolecularSurfaceCalcTask</name>
     <message>
@@ -375,64 +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="521"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="533"/>
         <source>No colors</source>
         <translation>No colors</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="529"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="541"/>
+        <source>UGENE Sanger</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="545"/>
         <source>Jalview</source>
         <translation>Jalview</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="531"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="569"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="547"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="585"/>
         <source>Percentage Identity</source>
         <translation>Percentage Identity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="532"/>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="570"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="548"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="586"/>
         <source>Percentage Identity (gray)</source>
         <translation>Percentage Identity (gray)</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="543"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
         <source>Zappo</source>
         <translation>Zappo</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="547"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="563"/>
         <source>Tailor</source>
         <translation>Tailor</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="551"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="567"/>
         <source>Hydrophobicity</source>
         <translation>Hydrophobicity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="555"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="571"/>
         <source>Helix propensity</source>
         <translation>Helix propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="559"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="575"/>
         <source>Strand propensity</source>
         <translation>Strand propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="563"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="579"/>
         <source>Turn propensity</source>
         <translation>Turn propensity</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="567"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="583"/>
         <source>Buried index</source>
         <translation>Buried index</translation>
     </message>
     <message>
-        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="572"/>
+        <location filename="../src/util_msaedit/color_schemes/MsaColorScheme.cpp" line="588"/>
         <source>Clustal X</source>
         <translation>Clustal X</translation>
     </message>
@@ -589,7 +607,7 @@ For every column selects the most rare symbol in the whole alignment with percen
 <context>
     <name>U2::SimpleAddToAlignmentTask</name>
     <message>
-        <location filename="../src/msa_alignment/SimpleAddingToAlignment.cpp" line="52"/>
+        <location filename="../src/msa_alignment/SimpleAddingToAlignment.cpp" line="51"/>
         <source>Align sequences to an existing alignment by UGENE started</source>
         <translation>Align sequences to an existing alignment by UGENE started</translation>
     </message>