X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=b3b2111540fecc0a369da12f8d9dce01630bf5d1;hb=9c00e25bfdf274009a471eba895f39e2fac4c0ac;hp=34595178c486bfbb913942cd0e948808dea16781;hpb=5f8a96e101d9e8bd2a35767588398ace4f3022ad;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3459517..b3b2111 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -27,22 +27,55 @@ import jalview.schemes.*;
 
 public class AnnotationFile
 {
-  StringBuffer text = new StringBuffer("JALVIEW_ANNOTATION\n"
-          + "# Created: " + new java.util.Date() + "\n\n");
+  public AnnotationFile()
+  {
+    init();
+  }
+
+  /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  /**
+   * set new line string and reset the output buffer
+   * 
+   * @param nl
+   */
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+    init();
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  StringBuffer text;
+
+  private void init()
+  {
+    text = new StringBuffer("JALVIEW_ANNOTATION"+newline + "# Created: "
+            + new java.util.Date() + newline + newline);
+    refSeq = null;
+    refSeqId = null;
+  }
 
   /**
    * convenience method for pre-2.4 feature files which have no view, hidden
    * columns or hidden row keywords.
    * 
    * @param annotations
-   * @param groups
+   * @param list
    * @param properties
    * @return feature file as a string.
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          Vector groups, Hashtable properties)
+          List<SequenceGroup> list, Hashtable properties)
   {
-    return printAnnotations(annotations, groups, properties, null);
+    return printAnnotations(annotations, list, properties, null);
 
   }
 
@@ -77,13 +110,13 @@ public class AnnotationFile
    * properties and views.
    * 
    * @param annotations
-   * @param groups
+   * @param list
    * @param properties
    * @param views
    * @return annotation file
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          Vector groups, Hashtable properties, ViewDef[] views)
+          List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
   {
     // TODO: resolve views issue : annotationFile could contain visible region,
     // or full data + hidden region specifications for a view.
@@ -118,7 +151,9 @@ public class AnnotationFile
         {
           if (refSeq != null)
           {
-            text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+            text.append(newline);
+            text.append("SEQUENCE_REF\tALIGNMENT");
+            text.append(newline);
           }
 
           refSeq = null;
@@ -129,7 +164,10 @@ public class AnnotationFile
           if (refSeq == null || refSeq != row.sequenceRef)
           {
             refSeq = row.sequenceRef;
-            text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+            text.append(newline);
+            text.append("SEQUENCE_REF\t");
+            text.append(refSeq.getName());
+            text.append(newline);
           }
         }
         // mark any group references for the row
@@ -138,7 +176,9 @@ public class AnnotationFile
 
           if (refGroup != null)
           {
-            text.append("\nGROUP_REF\tALIGNMENT\n");
+            text.append(newline);
+            text.append("GROUP_REF\tALIGNMENT");
+            text.append(newline);
           }
 
           refGroup = null;
@@ -148,7 +188,10 @@ public class AnnotationFile
           if (refGroup == null || refGroup != row.groupRef)
           {
             refGroup = row.groupRef;
-            text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");
+            text.append(newline);
+            text.append("GROUP_REF\t");
+            text.append(refGroup.getName());
+            text.append(newline);
           }
         }
 
@@ -194,16 +237,16 @@ public class AnnotationFile
 
           if (row.getThreshold() != null)
           {
-            graphLine
-                    .append("GRAPHLINE\t"
-                            + row.label
-                            + "\t"
-                            + row.getThreshold().value
-                            + "\t"
-                            + row.getThreshold().label
-                            + "\t"
-                            + jalview.util.Format.getHexString(row
-                                    .getThreshold().colour) + "\n");
+            graphLine.append("GRAPHLINE\t");
+            graphLine.append(row.label);
+            graphLine.append("\t");
+            graphLine.append(row.getThreshold().value);
+            graphLine.append("\t");
+            graphLine.append(row.getThreshold().label);
+            graphLine.append("\t");
+            graphLine.append(jalview.util.Format.getHexString(row
+                    .getThreshold().colour));
+            graphLine.append(newline);
           }
 
           if (row.graphGroup > -1)
@@ -308,25 +351,32 @@ public class AnnotationFile
         if (row.hasScore())
           text.append("\t" + row.score);
 
-        text.append("\n");
+        text.append(newline);
 
         if (color != null && color != java.awt.Color.black && oneColour)
         {
-          colours.append("COLOUR\t" + row.label + "\t"
-                  + jalview.util.Format.getHexString(color) + "\n");
+          colours.append("COLOUR\t");
+          colours.append(row.label);
+          colours.append("\t");
+          colours.append(jalview.util.Format.getHexString(color));
+          colours.append(newline);
         }
         if (row.scaleColLabel || row.showAllColLabels
                 || row.centreColLabels)
         {
-          rowprops.append("ROWPROPERTIES\t" + row.label);
-          rowprops.append("\tscaletofit=" + row.scaleColLabel);
-          rowprops.append("\tshowalllabs=" + row.showAllColLabels);
-          rowprops.append("\tcentrelabs=" + row.centreColLabels);
-          rowprops.append("\n");
+          rowprops.append("ROWPROPERTIES\t");
+          rowprops.append(row.label);
+          rowprops.append("\tscaletofit=");
+          rowprops.append(row.scaleColLabel);
+          rowprops.append("\tshowalllabs=");
+          rowprops.append(row.showAllColLabels);
+          rowprops.append("\tcentrelabs=");
+          rowprops.append(row.centreColLabels);
+          rowprops.append(newline);
         }
       }
 
-      text.append("\n");
+      text.append(newline);
 
       text.append(colours.toString());
       text.append(graphLine.toString());
@@ -336,25 +386,31 @@ public class AnnotationFile
         Enumeration en = graphGroup.elements();
         while (en.hasMoreElements())
         {
-          text.append(en.nextElement() + "\n");
+          text.append(en.nextElement());
+          text.append(newline);
         }
       }
       text.append(rowprops.toString());
     }
 
-    if (groups != null)
+    if (list != null)
     {
-      printGroups(groups);
+      printGroups(list);
     }
 
     if (properties != null)
     {
-      text.append("\n\nALIGNMENT");
+      text.append(newline);
+      text.append(newline);
+      text.append("ALIGNMENT");
       Enumeration en = properties.keys();
       while (en.hasMoreElements())
       {
         String key = en.nextElement().toString();
-        text.append("\t" + key + "=" + properties.get(key));
+        text.append("\t");
+        text.append(key);
+        text.append("=");
+        text.append(properties.get(key));
       }
       // TODO: output alignment visualization settings here if required
 
@@ -363,13 +419,11 @@ public class AnnotationFile
     return text.toString();
   }
 
-  public void printGroups(Vector sequenceGroups)
+  public void printGroups(List<SequenceGroup> list)
   {
-    SequenceGroup sg;
     SequenceI seqrep = null;
-    for (int i = 0; i < sequenceGroups.size(); i++)
+    for (SequenceGroup sg:list)
     {
-      sg = (SequenceGroup) sequenceGroups.elementAt(i);
       if (!sg.hasSeqrep())
       {
         text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
@@ -380,61 +434,90 @@ public class AnnotationFile
       else
       {
         seqrep = sg.getSeqrep();
-        text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");
-        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
-                + (seqrep.findPosition(sg.getStartRes())) + "\t"
-                + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");
+        text.append("SEQUENCE_REF\t");
+        text.append(seqrep.getName());
+        text.append(newline);
+        text.append("SEQUENCE_GROUP\t");
+        text.append(sg.getName());
+        text.append("\t");
+        text.append((seqrep.findPosition(sg.getStartRes())));
+        text.append("\t");
+        text.append((seqrep.findPosition(sg.getEndRes())));
+        text.append("\t");
+        text.append("-1\t");
       }
       for (int s = 0; s < sg.getSize(); s++)
       {
-        text.append(sg.getSequenceAt(s).getName() + "\t");
+        text.append(sg.getSequenceAt(s).getName());
+        text.append("\t");
       }
-
-      text.append("\nPROPERTIES\t" + sg.getName() + "\t");
+      text.append(newline);
+      text.append("PROPERTIES\t");
+      text.append(sg.getName());
+      text.append("\t");
 
       if (sg.getDescription() != null)
       {
-        text.append("description=" + sg.getDescription() + "\t");
+        text.append("description=");
+        text.append(sg.getDescription());
+        text.append("\t");
       }
       if (sg.cs != null)
       {
-        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)
-                + "\t");
+        text.append("colour=");
+        text.append(ColourSchemeProperty.getColourName(sg.cs));
+        text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {
-          text.append("pidThreshold=" + sg.cs.getThreshold());
+          text.append("pidThreshold=");
+          text.append(sg.cs.getThreshold());
         }
         if (sg.cs.conservationApplied())
         {
-          text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
+          text.append("consThreshold=");
+          text.append(sg.cs.getConservationInc());
+          text.append("\t");
         }
       }
-      text.append("outlineColour="
-              + jalview.util.Format.getHexString(sg.getOutlineColour())
-              + "\t");
-
-      text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
-      text.append("displayText=" + sg.getDisplayText() + "\t");
-      text.append("colourText=" + sg.getColourText() + "\t");
-      text.append("showUnconserved=" + sg.getShowNonconserved() + "\t");
+      text.append("outlineColour=");
+      text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+      text.append("\t");
+
+      text.append("displayBoxes=");
+      text.append(sg.getDisplayBoxes());
+      text.append("\t");
+      text.append("displayText=");
+      text.append(sg.getDisplayText());
+      text.append("\t");
+      text.append("colourText=");
+      text.append(sg.getColourText());
+      text.append("\t");
+      text.append("showUnconserved=");
+      text.append(sg.getShowNonconserved());
+      text.append("\t");
       if (sg.textColour != java.awt.Color.black)
       {
-        text.append("textCol1="
-                + jalview.util.Format.getHexString(sg.textColour) + "\t");
+        text.append("textCol1=");
+        text.append(jalview.util.Format.getHexString(sg.textColour));
+        text.append("\t");
       }
       if (sg.textColour2 != java.awt.Color.white)
       {
-        text.append("textCol2="
-                + jalview.util.Format.getHexString(sg.textColour2) + "\t");
+        text.append("textCol2=");
+        text.append(jalview.util.Format.getHexString(sg.textColour2));
+        text.append("\t");
       }
       if (sg.thresholdTextColour != 0)
       {
-        text.append("textColThreshold=" + sg.thresholdTextColour + "\t");
+        text.append("textColThreshold=");
+        text.append(sg.thresholdTextColour);
+        text.append("\t");
       }
       if (sg.idColour != null)
       {
-        text.append("idColour="
-                + jalview.util.Format.getHexString(sg.idColour) + "\t");
+        text.append("idColour=");
+        text.append(jalview.util.Format.getHexString(sg.idColour));
+        text.append("\t");
       }
       if (sg.isHidereps())
       {
@@ -447,9 +530,11 @@ public class AnnotationFile
       if (seqrep != null)
       {
         // terminate the last line and clear the sequence ref for the group
-        text.append("\nSEQUENCE_REF");
+        text.append(newline);
+        text.append("SEQUENCE_REF");
       }
-      text.append("\n\n");
+      text.append(newline);
+      text.append(newline);
 
     }
   }
@@ -502,6 +587,7 @@ public class AnnotationFile
   public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
           throws Exception
   {
+    boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
 
@@ -525,16 +611,11 @@ public class AnnotationFile
             if (aa[aai].autoCalculated)
             {
               // make a note of the name and description
-              autoAnnots
-                      .put(aa[aai].graph
-                              + "\t"
-                              + aa[aai].label
-                              + "\t"
-                              + aa[aai].description
-                              + "\t"
-                              + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef
-                                      .getDisplayId(true) : ""),
-                              new Integer(1));
+              autoAnnots.put(
+                      autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+                              (aa[aai].groupRef == null ? null
+                                      : aa[aai].groupRef.getName())),
+                      new Integer(1));
             }
           }
         }
@@ -583,22 +664,26 @@ public class AnnotationFile
         {
           // TODO: use graduated colour def'n here too
           colourAnnotations(al, st.nextToken(), st.nextToken());
+          modified = true;
           continue;
         }
 
         else if (token.equalsIgnoreCase("COMBINE"))
         {
           combineAnnotations(al, st);
+          modified = true;
           continue;
         }
         else if (token.equalsIgnoreCase("ROWPROPERTIES"))
         {
           addRowProperties(al, st);
+          modified = true;
           continue;
         }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
+          modified = true;
           continue;
         }
 
@@ -663,17 +748,20 @@ public class AnnotationFile
         else if (token.equalsIgnoreCase("PROPERTIES"))
         {
           addProperties(al, st);
+          modified = true;
           continue;
         }
 
         else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
         {
           setBelowAlignment(al, st);
+          modified = true;
           continue;
         }
         else if (token.equalsIgnoreCase("ALIGNMENT"))
         {
           addAlignmentDetails(al, st);
+          modified = true;
           continue;
         }
 
@@ -746,15 +834,8 @@ public class AnnotationFile
 
         annotation.score = score;
         if (!overrideAutoAnnot
-                && autoAnnots
-                        .containsKey(annotation.graph
-                                + "\t"
-                                + annotation.label
-                                + "\t"
-                                + annotation.description
-                                + "\t"
-                                + (refSeq != null ? refSeq
-                                        .getDisplayId(true) : "")))
+                && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+                        groupRef)))
         {
           // skip - we've already got an automatic annotation of this type.
           continue;
@@ -801,20 +882,19 @@ public class AnnotationFile
             ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
           }
         }
+        // and set modification flag
+        modified = true;
       }
       // Finally, resolve the groupRefs
       Enumeration en = groupRefRows.keys();
-      SequenceGroup theGroup = null;
-
+      
       while (en.hasMoreElements())
       {
         groupRef = (String) en.nextElement();
         boolean matched = false;
         // Resolve group: TODO: add a getGroupByName method to alignments
-        Vector grps = al.getGroups();
-        for (int g = 0, gSize = grps.size(); g < gSize; g++)
+        for (SequenceGroup theGroup : al.getGroups())
         {
-          theGroup = (SequenceGroup) grps.elementAt(g);
           if (theGroup.getName().equals(groupRef))
           {
             if (matched)
@@ -844,7 +924,15 @@ public class AnnotationFile
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
     }
-    return true;
+    return modified;
+  }
+
+  private Object autoAnnotsKey(AlignmentAnnotation annotation,
+          SequenceI refSeq, String groupRef)
+  {
+    return annotation.graph + "\t" + annotation.label + "\t"
+            + annotation.description + "\t"
+            + (refSeq != null ? refSeq.getDisplayId(true) : "");
   }
 
   Annotation parseAnnotation(String string, int graphStyle)
@@ -925,7 +1013,7 @@ public class AnnotationFile
         }
       }
       if (hasSymbols
-              && (token.equals("H") || token.equals("E") || token
+              && (token.equals("H") || token.equals("E") || token.equals("S") || token
                       .equals(" ")))
       {
         // Either this character represents a helix or sheet
@@ -1200,15 +1288,12 @@ public class AnnotationFile
     {
       return;
     }
-    SequenceGroup sg = null;
-
+    
     String name = st.nextToken();
-
-    Vector groups = al.getGroups();
-    for (int i = 0; i < groups.size(); i++)
+    SequenceGroup sg=null;
+    for (SequenceGroup _sg:al.getGroups())
     {
-      sg = (SequenceGroup) groups.elementAt(i);
-      if (sg.getName().equals(name))
+      if ((sg=_sg).getName().equals(name))
       {
         break;
       }
@@ -1250,7 +1335,7 @@ public class AnnotationFile
                   sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
-          c.verdict(false, 25);
+          c.verdict(false, 25); // TODO: refer to conservation percent threshold
 
           sg.cs.setConservation(c);
 
@@ -1384,7 +1469,7 @@ public class AnnotationFile
         else
         {
           sp.append(atos.substring(p));
-          sp.append("\n");
+          sp.append(newline);
         }
         p = cp + 1;
       } while (p > 0);