beginning of implementation of new properties for hide/show groups and sequence repre...

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d9fd871..1872f60 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -60,13 +60,15 @@ public class AnnotationFile
     public ColumnSelection hiddencols;\r
 \r
     public Vector visibleGroups;\r
-\r
+    public Hashtable hiddenRepSeqs;\r
+    \r
     public ViewDef(String viewname, HiddenSequences hidseqs,\r
-            ColumnSelection hiddencols)\r
+            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)\r
     {\r
       this.viewname = viewname;\r
       this.hidseqs = hidseqs;\r
       this.hiddencols = hiddencols;\r
+      this.hiddenRepSeqs = hiddenRepSeqs;\r
     }\r
   }\r
 \r
@@ -268,12 +270,23 @@ public class AnnotationFile
   public void printGroups(Vector sequenceGroups)\r
   {\r
     SequenceGroup sg;\r
+    SequenceI seqrep=null;\r
     for (int i = 0; i < sequenceGroups.size(); i++)\r
     {\r
       sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
-      text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
-              + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"\r
-              + "-1\t");\r
+      if (!sg.hasSeqrep())\r
+      {\r
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"\r
+                + "-1\t");\r
+        seqrep = null;\r
+      } else {\r
+        seqrep = sg.getSeqrep();\r
+        text.append("SEQUENCE_REF\t"+seqrep.getName()+"\n");\r
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+                + (seqrep.findPosition(sg.getStartRes())) + "\t" + (seqrep.findPosition(sg.getEndRes())) + "\t"\r
+                + "-1\t");\r
+      }\r
       for (int s = 0; s < sg.getSize(); s++)\r
       {\r
         text.append(sg.getSequenceAt(s).getName() + "\t");\r
@@ -318,14 +331,26 @@ public class AnnotationFile
       }\r
       if (sg.thresholdTextColour != 0)\r
       {\r
-        text.append("textColThreshold=" + sg.thresholdTextColour);\r
+        text.append("textColThreshold=" + sg.thresholdTextColour+"\t");\r
       }\r
       if (sg.idColour != null)\r
       {\r
         text.append("idColour="\r
                 + jalview.util.Format.getHexString(sg.idColour) + "\t");\r
       }\r
-\r
+      if (sg.isHidereps())\r
+      {\r
+        text.append("hide=true\t");\r
+      }\r
+      if (sg.isHideCols())\r
+      {\r
+        text.append("hidecols=true\t");\r
+      }\r
+      if (seqrep!=null)\r
+      {\r
+        // terminate the last line and clear the sequence ref for the group\r
+        text.append("\nSEQUENCE_REF");\r
+      }\r
       text.append("\n\n");\r
 \r
     }\r
@@ -752,13 +777,33 @@ public class AnnotationFile
 \r
     annotation.setThreshold(new GraphLine(value, label, colour));\r
   }\r
-\r
   void addGroup(AlignmentI al, StringTokenizer st)\r
   {\r
     SequenceGroup sg = new SequenceGroup();\r
     sg.setName(st.nextToken());\r
-    sg.setStartRes(Integer.parseInt(st.nextToken()) - 1);\r
-    sg.setEndRes(Integer.parseInt(st.nextToken()) - 1);\r
+    String rng ="";\r
+    try {\r
+      rng = st.nextToken();\r
+      if (rng.length()>0 && !rng.startsWith("*"))\r
+      {\r
+        sg.setStartRes(Integer.parseInt(rng) - 1);\r
+      } else {\r
+        sg.setStartRes(0);\r
+      }\r
+      rng = st.nextToken();\r
+      if (rng.length()>0 && !rng.startsWith("*"))\r
+      {\r
+        sg.setEndRes(Integer.parseInt(rng) - 1);\r
+      } else {\r
+        sg.setEndRes(al.getWidth()-1);\r
+      }\r
+    } catch (Exception e)\r
+    {\r
+      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.");\r
+      // assume group is full width\r
+      sg.setStartRes(0);\r
+      sg.setEndRes(al.getWidth()-1);\r
+    }\r
 \r
     String index = st.nextToken();\r
     if (index.equals("-1"))\r
@@ -810,6 +855,7 @@ public class AnnotationFile
     {\r
       sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\r
       sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);\r
+      sg.setSeqrep(refSeq);\r
     }\r
 \r
     if (sg.getSize() > 0)\r
@@ -917,6 +963,16 @@ public class AnnotationFile
           sg.setIdColour((def = new UserColourScheme(value))\r
                   .findColour('A'));\r
         }\r
+        else if (key.equalsIgnoreCase("hide"))\r
+        {\r
+          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847\r
+          sg.setHidereps(true);\r
+        }\r
+        else if (key.equalsIgnoreCase("hidecols"))\r
+        {\r
+          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847\r
+          sg.setHideCols(true);\r
+        }\r
         sg.recalcConservation();\r
       }\r
       if (sg.cs == null)\r