From: jprocter <Jim Procter>
Date: Fri, 21 Jan 2011 17:05:43 +0000 (+0000)
Subject: relaxed ID matching parameter JAL-753
X-Git-Tag: Release_2_7~282
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=20c600dc8c628f5a82cc32b1fe026291756f1d8e;p=jalview.git

relaxed ID matching parameter JAL-753
---

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 64bb539..34253cb 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -20,6 +20,7 @@ package jalview.io;
 import java.io.*;
 import java.util.*;
 
+import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.util.Format;
@@ -70,28 +71,60 @@ public class FeaturesFile extends AlignFile
   }
 
   /**
-   * The Application can render HTML, but the applet will remove HTML tags and
-   * replace links with %LINK% Both need to read links in HTML however
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
+   * Parse GFF or sequence features file using case-independent matching, discarding URLs
+   * @param align - alignment/dataset containing sequences that are to be annotated
+   * @param colours - hashtable to store feature colour definitions
+   * @param removeHTML - process html strings into plain text
+   * @return true if features were added
    */
   public boolean parse(AlignmentI align, Hashtable colours,
           boolean removeHTML)
   {
-    return parse(align, colours, null, removeHTML);
+    return parse(align, colours, null, removeHTML, false);
   }
 
   /**
-   * The Application can render HTML, but the applet will remove HTML tags and
-   * replace links with %LINK% Both need to read links in HTML however
-   * 
-   * @throws IOException
-   *           DOCUMENT ME!
+   * Parse GFF or sequence features file optionally using case-independent matching, discarding URLs
+   * @param align - alignment/dataset containing sequences that are to be annotated
+   * @param colours - hashtable to store feature colour definitions
+   * @param removeHTML - process html strings into plain text
+   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
+   * @return true if features were added
+   */
+  public boolean parse(AlignmentI align, 
+          Hashtable colours, boolean removeHTML, boolean relaxedIdMatching)
+  {
+    return parse(align, colours, null, removeHTML, relaxedIdMatching);
+  }
+
+  /**
+   * Parse GFF or sequence features file optionally using case-independent matching
+   * @param align - alignment/dataset containing sequences that are to be annotated
+   * @param colours - hashtable to store feature colour definitions
+   * @param featureLink - hashtable to store associated URLs 
+   * @param removeHTML - process html strings into plain text
+   * @return true if features were added
    */
   public boolean parse(AlignmentI align, Hashtable colours,
           Hashtable featureLink, boolean removeHTML)
   {
+    return parse(align, colours, featureLink, removeHTML, false);
+  }
+
+  /**
+  /**
+   * Parse GFF or sequence features file 
+   * @param align - alignment/dataset containing sequences that are to be annotated
+   * @param colours - hashtable to store feature colour definitions
+   * @param featureLink - hashtable to store associated URLs 
+   * @param removeHTML - process html strings into plain text
+   * @param relaxedIdmatching - when true, ID matches to compound sequence IDs are allowed
+   * @return true if features were added
+   */
+  public boolean parse(AlignmentI align,
+          Hashtable colours, Hashtable featureLink, boolean removeHTML, boolean relaxedIdmatching)
+  {
+
     String line = null;
     try
     {
@@ -369,7 +402,7 @@ public class FeaturesFile extends AlignFile
             // Still possible this is an old Jalview file,
             // which does not have type colours at the beginning
             seqId = token = st.nextToken();
-            seq = align.findName(seqId, true);
+            seq = findName(align, seqId, relaxedIdmatching);
             if (seq != null)
             {
               desc = st.nextToken();
@@ -478,7 +511,7 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = align.findName(seqId = token, true);
+            seq = findName(align, seqId = token, relaxedIdmatching);
             st.nextToken();
           }
           else
@@ -548,17 +581,52 @@ public class FeaturesFile extends AlignFile
           GFFFile = false;
         }
       }
+      resetMatcher();
     } catch (Exception ex)
     {
       System.out.println(line);
       System.out.println("Error parsing feature file: " + ex + "\n" + line);
       ex.printStackTrace(System.err);
+      resetMatcher();
       return false;
     }
 
     return true;
   }
 
+  private AlignmentI lastmatchedAl = null;
+
+  private SequenceIdMatcher matcher = null;
+
+  /**
+   * clear any temporary handles used to speed up ID matching
+   */
+  private void resetMatcher()
+  {
+    lastmatchedAl = null;
+    matcher = null;
+  }
+
+  private SequenceI findName(AlignmentI align, String seqId,
+          boolean relaxedIdMatching)
+  {
+    SequenceI match = null;
+    if (relaxedIdMatching)
+    {
+      if (lastmatchedAl != align)
+      {
+        matcher = new SequenceIdMatcher(
+                (lastmatchedAl = align).getSequencesArray());
+      }
+      match = matcher.findIdMatch(seqId);
+    }
+    else
+    {
+      match = align.findName(seqId, true);
+    }
+    return match;
+  }
+
   public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
   {
     if (sf.getDescription() == null)
@@ -929,19 +997,18 @@ public class FeaturesFile extends AlignFile
           out.append(source);
           out.append("\t");
           out.append(next[j].type);
-          out.append( "\t");
-          out.append(  next[j].begin );
           out.append("\t");
-          out.append(
-                  next[j].end);
-          out.append( "\t");
-          out.append( next[j].score);
-          out.append( "\t");
+          out.append(next[j].begin);
+          out.append("\t");
+          out.append(next[j].end);
+          out.append("\t");
+          out.append(next[j].score);
+          out.append("\t");
 
           if (next[j].getValue("STRAND") != null)
           {
             out.append(next[j].getValue("STRAND"));
-            out.append( "\t");
+            out.append("\t");
           }
           else
           {
@@ -956,7 +1023,8 @@ public class FeaturesFile extends AlignFile
           {
             out.append(".");
           }
-          // TODO: verify/check GFF - should there be a /t here before attribute output ?
+          // TODO: verify/check GFF - should there be a /t here before attribute
+          // output ?
 
           if (next[j].getValue("ATTRIBUTES") != null)
           {
@@ -989,4 +1057,5 @@ public class FeaturesFile extends AlignFile
   {
     return "USE printGFFFormat() or printJalviewFormat()";
   }
+
 }
diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index 5e5c446..f4fe55b 100644
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -148,6 +148,8 @@ public class JalviewDataset
    */
   Hashtable seqDetails;
 
+  public boolean relaxedIdMatching=false;
+
   public JalviewDataset()
   {
     seqDetails = new Hashtable();
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 787a88f..97802f3 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -133,8 +133,8 @@ public class ParsePackedSet
         try
         {
           jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
-          context.updateSetModified(ff.parse(context.getLastAlignment(),
-                  context.featureColours, false));
+          context.updateSetModified(ff.parse(context.getLastAlignment(), 
+                  context.featureColours, false, context.relaxedIdMatching));
         } catch (Exception e)
         {
           errmsg = ("Failed to parse the Features file associated with the alignment.");