X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=d4284a24e8612682f3b7492c856a3bc332c5f8e6;hb=329abf57c756ac530604dce9136045b0bd5ffaca;hp=aeaf2f3fdaa5a6672352c84629b94607b7217dee;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index aeaf2f3..d4284a2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -27,8 +27,41 @@ 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
@@ -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());
@@ -336,7 +386,8 @@ 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());
@@ -349,12 +400,17 @@ public class AnnotationFile
 
     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
 
@@ -380,61 +436,90 @@ 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.getShowunconserved() + "\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 +532,11 @@ 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);
 
     }
   }
@@ -461,13 +548,9 @@ public class AnnotationFile
   public boolean readAnnotationFile(AlignmentI al, String file,
           String protocol)
   {
-    String groupRef = null;
-    Hashtable groupRefRows = new Hashtable();
-
-    Hashtable autoAnnots = new Hashtable();
+    BufferedReader in = null;
     try
     {
-      BufferedReader in = null;
       if (protocol.equals(AppletFormatAdapter.FILE))
       {
         in = new BufferedReader(new FileReader(file));
@@ -489,7 +572,29 @@ public class AnnotationFile
           in = new BufferedReader(new java.io.InputStreamReader(is));
         }
       }
+      if (in != null)
+      {
+        return parseAnnotationFrom(al, in);
+      }
+
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Problem reading annotation file: " + ex);
+      return false;
+    }
+    return false;
+  }
+
+  public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+          throws Exception
+  {
+    boolean modified = false;
+    String groupRef = null;
+    Hashtable groupRefRows = new Hashtable();
 
+    Hashtable autoAnnots = new Hashtable();
+    {
       String line, label, description, token;
       int graphStyle, index;
       int refSeqIndex = 1;
@@ -508,14 +613,11 @@ 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));
             }
           }
         }
@@ -564,22 +666,26 @@ 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;
         }
 
@@ -644,17 +750,20 @@ 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;
         }
 
@@ -727,15 +836,8 @@ 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;
@@ -782,6 +884,8 @@ public class AnnotationFile
             ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
           }
         }
+        // and set modification flag
+        modified = true;
       }
       // Finally, resolve the groupRefs
       Enumeration en = groupRefRows.keys();
@@ -824,13 +928,16 @@ public class AnnotationFile
         }
         ((Vector) groupRefRows.get(groupRef)).removeAllElements();
       }
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-      System.out.println("Problem reading annotation file: " + ex);
-      return false;
     }
-    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)
@@ -982,45 +1089,55 @@ public class AnnotationFile
     int graphGroup = -1;
     String group = st.nextToken();
     // First make sure we are not overwriting the graphIndex
-    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
-    {
-      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
-      {
-        graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
-        al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
-        break;
-      }
-    }
-
-    // Now update groups
-    while (st.hasMoreTokens())
+    if (al.getAlignmentAnnotation() != null)
     {
-      group = st.nextToken();
       for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
         {
+          graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
           al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
           break;
         }
       }
+
+      // Now update groups
+      while (st.hasMoreTokens())
+      {
+        group = st.nextToken();
+        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+        {
+          if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+          {
+            al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+            break;
+          }
+        }
+      }
+    }
+    else
+    {
+      System.err
+              .println("Couldn't combine annotations. None are added to alignment yet!");
     }
   }
 
   void addLine(AlignmentI al, StringTokenizer st)
   {
     String group = st.nextToken();
-    AlignmentAnnotation annotation = null;
-
-    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation annotation = null, alannot[] = al
+            .getAlignmentAnnotation();
+    if (alannot != null)
     {
-      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      for (int i = 0; i < alannot.length; i++)
       {
-        annotation = al.getAlignmentAnnotation()[i];
-        break;
+        if (alannot[i].label.equalsIgnoreCase(group))
+        {
+          annotation = alannot[i];
+          break;
+        }
       }
     }
-
     if (annotation == null)
     {
       return;
@@ -1111,9 +1228,7 @@ public class AnnotationFile
         }
         else
         {
-          sg
-                  .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
-                          false);
+          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
         }
       }
     }
@@ -1153,13 +1268,16 @@ public class AnnotationFile
         centerlab = Boolean.valueOf(value).booleanValue();
       }
       AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
-      for (int i = 0; i < alr.length; i++)
+      if (alr != null)
       {
-        if (alr[i].label.equalsIgnoreCase(label))
+        for (int i = 0; i < alr.length; i++)
         {
-          alr[i].centreColLabels = centerlab;
-          alr[i].scaleColLabel = scaletofit;
-          alr[i].showAllColLabels = showalllabs;
+          if (alr[i].label.equalsIgnoreCase(label))
+          {
+            alr[i].centreColLabels = centerlab;
+            alr[i].scaleColLabel = scaletofit;
+            alr[i].showAllColLabels = showalllabs;
+          }
         }
       }
     }
@@ -1221,8 +1339,8 @@ public class AnnotationFile
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
           Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(null), sg
-                          .getStartRes(), sg.getEndRes() + 1);
+                  ResidueProperties.propHash, 3, sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25);
@@ -1240,7 +1358,7 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("showUnconserved"))
         {
-          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());
+          sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
         }
         else if (key.equalsIgnoreCase("displayText"))
         {
@@ -1290,19 +1408,35 @@ public class AnnotationFile
   void setBelowAlignment(AlignmentI al, StringTokenizer st)
   {
     String token;
-    AlignmentAnnotation aa;
+    AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
+    if (ala == null)
+    {
+      System.err
+              .print("Warning - no annotation to set below for sequence associated annotation:");
+    }
     while (st.hasMoreTokens())
     {
       token = st.nextToken();
-      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      if (ala == null)
       {
-        aa = al.getAlignmentAnnotation()[i];
-        if (aa.sequenceRef == refSeq && aa.label.equals(token))
+        System.err.print(" " + token);
+      }
+      else
+      {
+        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
         {
-          aa.belowAlignment = true;
+          aa = al.getAlignmentAnnotation()[i];
+          if (aa.sequenceRef == refSeq && aa.label.equals(token))
+          {
+            aa.belowAlignment = true;
+          }
         }
       }
     }
+    if (ala == null)
+    {
+      System.err.print("\n");
+    }
   }
 
   void addAlignmentDetails(AlignmentI al, StringTokenizer st)
@@ -1343,7 +1477,7 @@ public class AnnotationFile
         else
         {
           sp.append(atos.substring(p));
-          sp.append("\n");
+          sp.append(newline);
         }
         p = cp + 1;
       } while (p > 0);