When comparing LastModified times, allow them to differ by up to 2 se…

…conds

Notify the user when re-creating suffix array files or the .canno file

src/main/java/edu/ucsd/msjava/msdbsearch/CompactFastaSequence.java

@@ -123,16 +123,60 @@ private CompactFastaSequence(String filepath, String alphabet) {
             seqIdSignature = readSequence();
         }
 
-        if (metaIdSignature == null || seqIdSignature == null
-                || metaIdSignature.getFormatId() != COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID
-                || seqIdSignature.getFormatId() != COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID
-                || metaIdSignature.getId() != seqIdSignature.getId()
-                || metaIdSignature.getLastModified() != lastModified
-                || seqIdSignature.getLastModified() != lastModified
-                ) {
+        boolean indexingRequired = false;
+
+        if (metaIdSignature == null || seqIdSignature == null) {
+            System.out.println("Re-creating the .canno file since metaIdSignature is null or seqIdSignature is null");
+            indexingRequired = true;
+        }
+
+        if (metaIdSignature.getFormatId() != COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID) {
+            System.out.println("Re-creating the .canno file since the metaIdSignature is not " +
+                    COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID + ", it is " + metaIdSignature.getFormatId());
+            indexingRequired = true;
+        }
+
+        if (seqIdSignature.getFormatId() != COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID) {
+            System.out.println("Re-creating the .canno file since the seqIdSignature is not " +
+                    COMPACT_FASTA_SEQUENCE_FILE_FORMAT_ID + ", it is " + seqIdSignature.getFormatId());
+            indexingRequired = true;
+        }
+
+        if (metaIdSignature.getId() != seqIdSignature.getId()) {
+            System.out.println("Re-creating the .canno file since the metaIdSignature ID " +
+                    "doesn't match seqIdSignature ID: " +
+                    metaIdSignature.getId() + " vs. " + seqIdSignature.getId());
+            indexingRequired = true;
+        }
+
+        if (metaIdSignature.getLastModified() != seqIdSignature.getLastModified()) {
+            System.out.println("Re-creating the .canno file since metaIdSignature LastModified " +
+                    "doesn't match seqIdSignature LastModified: " +
+                    metaIdSignature.getLastModified() + " vs. " + seqIdSignature.getLastModified());
+            indexingRequired = true;
+        }
+
+        if (!CompactSuffixArray.NearlyEqualFileTimes(metaIdSignature.getLastModified(), lastModified)) {
+            System.out.println("Re-creating the .canno file since metaIdSignature LastModified " +
+                    "is not within 2 seconds of the file modification time on disk: " +
+                    "Expected " + metaIdSignature.getLastModified() + " but actually " + lastModified);
+            indexingRequired = true;
+        }
+
+        if (indexingRequired) {
             createObjectFromRawFile(filepath, alphabet);
             metaIdSignature = readMetaInfo();
             seqIdSignature = readSequence();
+        } else {
+            /*
+            System.out.println("Metadata matches; no need to re-index");
+
+            System.out.println("metaIdSignature ID: " + metaIdSignature.getId());
+            System.out.println("seqIdSignature ID:  " + seqIdSignature.getId());
+            System.out.println("metaIdSignature LastModified: " + metaIdSignature.getLastModified());
+            System.out.println("seqIdSignature LastModified:  " + seqIdSignature.getLastModified());
+            System.out.println("FASTA LastModified on disk:   " + lastModified + " for " + filepath);
+            */
         }
 
         initializeAlphabet(this.alphabetString);

src/main/java/edu/ucsd/msjava/msdbsearch/CompactSuffixArray.java

@@ -148,15 +148,30 @@ private boolean isCompactSuffixArrayValid(long lastModified) {
                 int id = raf.readInt();
                 raf.close();
 
-                if (lastModifiedRecorded != lastModified || id != COMPACT_SUFFIX_ARRAY_FILE_FORMAT_ID)
+                if (!NearlyEqualFileTimes(lastModifiedRecorded, lastModified)) {
+                    System.out.println("Re-creating suffix array files since the cached LastModified time is not within 2 seconds " +
+                            "of the LastModified time of the sequence file:" +
+                            " Time cached in " + f.getName() + " is " + lastModifiedRecorded +
+                            " while the sequence file has " + lastModified);
                     return false;
+                }
+
+                if (id != COMPACT_SUFFIX_ARRAY_FILE_FORMAT_ID) {
+                    System.out.println("Re-creating suffix array files since " + f.getName() +
+                            " has file format ID " + id + " instead of " + COMPACT_SUFFIX_ARRAY_FILE_FORMAT_ID);
+                    return false;
+                }
+
             } catch (FileNotFoundException e) {
                 e.printStackTrace();
             } catch (IOException e) {
                 e.printStackTrace();
             }
         }
 
+        //System.out.println("LastModified times in the existing csarr and cnlcp files " +
+        //        "match the LastModified time of the sequence file (" + lastModified + ")");
+
         return true;
     }
 
@@ -484,4 +499,23 @@ public void measureNominalMassError(AminoAcidSet aaSet) throws Exception {
         indices.close();
         nlcps.close();
     }
+
+    /**
+     * Compares two timestamps (typically the lastModified value for a file)
+     * If they agree within 2 seconds, returns True, otherwise false
+     * @param time1 First file time (milliseconds since 1/1/1970)
+     * @param time2 Second file time (milliseconds since 1/1/1970)
+     * @return True if the times agree within 2 seconds
+     */
+    public static boolean NearlyEqualFileTimes(long time1, long time2)
+    {
+        double timeDiffSeconds = (time1 - time2) / 1000.0;
+        if (Math.abs(timeDiffSeconds) <= 2.05)
+        {
+            return true;
+        }
+
+        return false;
+    }
+
 }