X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ce1afc274bf08f745c6fabf3882aa7ff8ec8279f;hb=1660a4fe03b8dda74b008ae4de2d804f8044a463;hp=7f71df18f9bb06686b879766426cde6203dd9dec;hpb=67b2671b1ded591a6f8eb7f13d319e58f993df77;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 7f71df1..ce1afc2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -60,8 +60,9 @@ public class AnnotationFile
     public ColumnSelection hiddencols;
 
     public Vector visibleGroups;
+
     public Hashtable hiddenRepSeqs;
-    
+
     public ViewDef(String viewname, HiddenSequences hidseqs,
             ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
     {
@@ -71,10 +72,18 @@ public class AnnotationFile
       this.hiddenRepSeqs = hiddenRepSeqs;
     }
   }
-
+  /**
+   * Prepare an annotation file given a set of annotations, groups, alignment properties and views. 
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @param views
+   * @return annotation file
+   */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           Vector groups, Hashtable properties, ViewDef[] views)
   {
+    // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -84,7 +93,7 @@ public class AnnotationFile
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
-
+      StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
 
       java.awt.Color color;
@@ -116,19 +125,43 @@ public class AnnotationFile
           refSeq = row.sequenceRef;
           text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
         }
+        boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
+        // lookahead to check what the annotation row object actually contains.
+        for (int j = 0; row.annotations != null
+                && j < row.annotations.length
+                && (!hasGlyphs || !hasLabels || !hasValues); j++)
+        {
+          if (row.annotations[j] != null)
+          {
+            hasLabels |= (row.annotations[j].displayCharacter != null
+                    && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
+                    .equals(" "));
+            hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
+            hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+                                                                  // be
+                                                                  // rendered..
+            hasText |= (row.annotations[j].description != null && row.annotations[j].description
+                    .length() > 0);
+          }
+        }
 
         if (row.graph == AlignmentAnnotation.NO_GRAPH)
         {
           text.append("NO_GRAPH\t");
+          hasValues = false; // only secondary structure
+          // hasLabels = false; // and annotation description string.
         }
         else
         {
           if (row.graph == AlignmentAnnotation.BAR_GRAPH)
           {
             text.append("BAR_GRAPH\t");
+            hasGlyphs = false; // no secondary structure
+
           }
           else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
           {
+            hasGlyphs = false; // no secondary structure
             text.append("LINE_GRAPH\t");
           }
 
@@ -165,7 +198,6 @@ public class AnnotationFile
         {
           text.append(row.description + "\t");
         }
-
         for (int j = 0; row.annotations != null
                 && j < row.annotations.length; j++)
         {
@@ -178,33 +210,54 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (row.annotations[j].secondaryStructure != ' ')
+            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... 
             {
+
               text.append(comma + row.annotations[j].secondaryStructure);
               comma = ",";
             }
-            if (row.annotations[j].displayCharacter != null
-                    && row.annotations[j].displayCharacter.length() > 0
-                    && !row.annotations[j].displayCharacter.equals(" "))
+            if (hasValues)
             {
-              text.append(comma + row.annotations[j].displayCharacter);
+              if (row.annotations[j].value != Float.NaN)
+              {
+                text.append(comma + row.annotations[j].value);
+              }
+              else
+              {
+                System.err.println("Skipping NaN - not valid value.");
+                text.append(comma + 0f);// row.annotations[j].value);
+              }
               comma = ",";
             }
-
-            if (row.annotations[j] != null)
+            if (hasLabels)
             {
-              if (color != null && !color.equals(row.annotations[j].colour))
+              // TODO: labels are emitted after values for bar graphs.
+              if // empty labels are allowed, so
+              (row.annotations[j].displayCharacter != null
+                      && row.annotations[j].displayCharacter.length() > 0
+                      && !row.annotations[j].displayCharacter.equals(" "))
               {
-                oneColour = false;
+                text.append(comma + row.annotations[j].displayCharacter);
+                comma = ",";
               }
-
-              color = row.annotations[j].colour;
-              if (row.annotations[j].value != 0f
-                      && row.annotations[j].value != Float.NaN)
+            }
+            if (hasText)
+            {
+              if (row.annotations[j].description != null
+                      && row.annotations[j].description.length() > 0
+                      && !row.annotations[j].description
+                              .equals(row.annotations[j].displayCharacter))
               {
-                text.append(comma + row.annotations[j].value);
+                text.append(comma + row.annotations[j].description);
+                comma = ",";
               }
             }
+            if (color != null && !color.equals(row.annotations[j].colour))
+            {
+              oneColour = false;
+            }
+
+            color = row.annotations[j].colour;
 
             if (row.annotations[j].colour != null
                     && row.annotations[j].colour != java.awt.Color.black)
@@ -214,6 +267,7 @@ public class AnnotationFile
                       + jalview.util.Format
                               .getHexString(row.annotations[j].colour)
                       + "]");
+              comma = ",";
             }
           }
           text.append("|");
@@ -229,7 +283,14 @@ public class AnnotationFile
           colours.append("COLOUR\t" + row.label + "\t"
                   + jalview.util.Format.getHexString(color) + "\n");
         }
-
+        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");
+        }
       }
 
       text.append("\n");
@@ -245,6 +306,7 @@ public class AnnotationFile
           text.append(en.nextElement() + "\n");
         }
       }
+      text.append(rowprops.toString());
     }
 
     if (groups != null)
@@ -271,22 +333,24 @@ public class AnnotationFile
   public void printGroups(Vector sequenceGroups)
   {
     SequenceGroup sg;
-    SequenceI seqrep=null;
+    SequenceI seqrep = null;
     for (int i = 0; i < sequenceGroups.size(); i++)
     {
       sg = (SequenceGroup) sequenceGroups.elementAt(i);
       if (!sg.hasSeqrep())
       {
         text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
-                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"
-                + "-1\t");
+                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+                + "\t" + "-1\t");
         seqrep = null;
-      } else {
+      }
+      else
+      {
         seqrep = sg.getSeqrep();
-        text.append("SEQUENCE_REF\t"+seqrep.getName()+"\n");
+        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");
+                + (seqrep.findPosition(sg.getStartRes())) + "\t"
+                + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");
       }
       for (int s = 0; s < sg.getSize(); s++)
       {
@@ -319,7 +383,7 @@ public class AnnotationFile
       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("showUnconserved=" + sg.getShowunconserved() + "\t");
       if (sg.textColour != java.awt.Color.black)
       {
         text.append("textCol1="
@@ -332,7 +396,7 @@ public class AnnotationFile
       }
       if (sg.thresholdTextColour != 0)
       {
-        text.append("textColThreshold=" + sg.thresholdTextColour+"\t");
+        text.append("textColThreshold=" + sg.thresholdTextColour + "\t");
       }
       if (sg.idColour != null)
       {
@@ -347,7 +411,7 @@ public class AnnotationFile
       {
         text.append("hidecols=true\t");
       }
-      if (seqrep!=null)
+      if (seqrep != null)
       {
         // terminate the last line and clear the sequence ref for the group
         text.append("\nSEQUENCE_REF");
@@ -449,7 +513,11 @@ public class AnnotationFile
           combineAnnotations(al, st);
           continue;
         }
-
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
@@ -566,7 +634,7 @@ public class AnnotationFile
             }
             else
             {
-              annotations[index++] = parseAnnotation(token);
+              annotations[index++] = parseAnnotation(token, graphStyle);
               emptyColumn = false;
             }
           }
@@ -589,7 +657,8 @@ public class AnnotationFile
             // TODO: verify that undo/redo with 1:many sequence associated
             // annotations can be undone correctly
             AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
-            annotation.createSequenceMapping(referedSeq, refSeqIndex, false);
+            annotation
+                    .createSequenceMapping(referedSeq, refSeqIndex, false);
             annotation.adjustForAlignment();
             referedSeq.addAlignmentAnnotation(annotation);
             al.addAnnotation(annotation);
@@ -620,12 +689,13 @@ public class AnnotationFile
     return true;
   }
 
-  Annotation parseAnnotation(String string)
+  Annotation parseAnnotation(String string, int graphStyle)
   {
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure
     String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
-    boolean parsedValue = false;
+    boolean parsedValue = false, dcset = false;
 
     // find colour here
     java.awt.Color colour = null;
@@ -636,25 +706,40 @@ public class AnnotationFile
       UserColourScheme ucs = new UserColourScheme();
 
       colour = ucs.getColourFromString(string.substring(i + 1, j));
-
+      if ( i>0 && string.charAt(i-1)==',')
+      {
+        // clip the preceding comma as well
+        i--;
+      }
       string = string.substring(0, i) + string.substring(j + 1);
     }
 
-    StringTokenizer st = new StringTokenizer(string, ",");
+    StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
+    boolean seenContent=false;
     while (st.hasMoreTokens())
     {
       token = st.nextToken().trim();
-      if (token.length() == 0)
+      if (token.equals(","))
       {
+        if (!seenContent && parsedValue && !dcset)
+        {
+          // allow the value below the bar/line to be empty
+          dcset = true;
+          displayChar = " ";
+        }
+        seenContent = false;
         continue;
+      } else {
+        seenContent = true;
       }
 
       if (!parsedValue)
       {
         try
         {
-          displayChar = token;
+          displayChar = token; 
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
@@ -663,7 +748,7 @@ public class AnnotationFile
         }
       }
 
-      if (token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -679,7 +764,10 @@ public class AnnotationFile
       }
 
     }
-
+//    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    {
+//      displayChar = " "; // empty display char symbol.
+//    }
     if (displayChar != null && displayChar.length() > 1 && desc != null
             && desc.length() == 1)
     {
@@ -779,32 +867,40 @@ public class AnnotationFile
 
     annotation.setThreshold(new GraphLine(value, label, colour));
   }
+
   void addGroup(AlignmentI al, StringTokenizer st)
   {
     SequenceGroup sg = new SequenceGroup();
     sg.setName(st.nextToken());
-    String rng ="";
-    try {
+    String rng = "";
+    try
+    {
       rng = st.nextToken();
-      if (rng.length()>0 && !rng.startsWith("*"))
+      if (rng.length() > 0 && !rng.startsWith("*"))
       {
         sg.setStartRes(Integer.parseInt(rng) - 1);
-      } else {
+      }
+      else
+      {
         sg.setStartRes(0);
       }
       rng = st.nextToken();
-      if (rng.length()>0 && !rng.startsWith("*"))
+      if (rng.length() > 0 && !rng.startsWith("*"))
       {
         sg.setEndRes(Integer.parseInt(rng) - 1);
-      } else {
-        sg.setEndRes(al.getWidth()-1);
+      }
+      else
+      {
+        sg.setEndRes(al.getWidth() - 1);
       }
     } catch (Exception e)
     {
-      System.err.println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"+rng+"' - assuming alignment width for group.");
+      System.err
+              .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+                      + rng + "' - assuming alignment width for group.");
       // assume group is full width
       sg.setStartRes(0);
-      sg.setEndRes(al.getWidth()-1);
+      sg.setEndRes(al.getWidth() - 1);
     }
 
     String index = st.nextToken();
@@ -866,6 +962,35 @@ public class AnnotationFile
     }
   }
 
+  void addRowProperties(AlignmentI al, StringTokenizer st)
+  {
+    String label = st.nextToken(),keyValue,key,value;
+    boolean scaletofit=false,centerlab=false,showalllabs=false;
+    while (st.hasMoreTokens()) {
+      keyValue=st.nextToken();
+      key = keyValue.substring(0, keyValue.indexOf("="));
+      value = keyValue.substring(keyValue.indexOf("=") + 1);
+      if (key.equalsIgnoreCase("scaletofit")) {
+        scaletofit = Boolean.valueOf(value).booleanValue();
+      }
+        if (key.equalsIgnoreCase("showalllabs")) {
+          showalllabs = Boolean.valueOf(value).booleanValue();
+        }
+        if (key.equalsIgnoreCase("centrelabs")) {
+          centerlab = Boolean.valueOf(value).booleanValue();
+    }
+        AlignmentAnnotation[] alr = al.getAlignmentAnnotation(); 
+        for (int i = 0; i < alr.length; i++)
+        {
+          if (alr[i].label.equalsIgnoreCase(label))
+          {
+            alr[i].centreColLabels = centerlab;
+            alr[i].scaleColLabel = scaletofit;
+            alr[i].showAllColLabels = showalllabs;
+          }
+        }
+    }
+  }
   void addProperties(AlignmentI al, StringTokenizer st)
   {