X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=9a21fbb2e855a60b79421c3459ec43b4cee80c2c;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=3d42475fb3dfe765def8761c77bb28eef6777ee0;hpb=db7a726e4cf2c7d5f650085bd07b7f19254688e9;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3d42475..9a21fbb 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 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,6 +14,7 @@
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -131,7 +132,8 @@ public class AnnotationFile
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable graphGroup = new Hashtable();
+ Hashtable graphGroup = new Hashtable();
+ Hashtable graphGroup_refs = new Hashtable();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
@@ -147,54 +149,13 @@ public class AnnotationFile
color = null;
oneColour = true;
-
- if (row.sequenceRef == null)
- {
- if (refSeq != null)
- {
- text.append(newline);
- text.append("SEQUENCE_REF\tALIGNMENT");
- text.append(newline);
- }
-
- refSeq = null;
- }
-
- else
- {
- if (refSeq == null || refSeq != row.sequenceRef)
- {
- refSeq = row.sequenceRef;
- text.append(newline);
- text.append("SEQUENCE_REF\t");
- text.append(refSeq.getName());
- text.append(newline);
- }
- }
+
+ // mark any sequence references for the row
+ writeSequence_Ref(refSeq ,row.sequenceRef);
+ refSeq = row.sequenceRef;
// mark any group references for the row
- if (row.groupRef == null)
- {
-
- if (refGroup != null)
- {
- text.append(newline);
- text.append("GROUP_REF\tALIGNMENT");
- text.append(newline);
- }
-
- refGroup = null;
- }
- else
- {
- if (refGroup == null || refGroup != row.groupRef)
- {
- refGroup = row.groupRef;
- text.append(newline);
- text.append("GROUP_REF\t");
- text.append(refGroup.getName());
- text.append(newline);
- }
- }
+ writeGroup_Ref(refGroup, row.groupRef);
+ refGroup = row.groupRef;
boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
// lookahead to check what the annotation row object actually contains.
@@ -253,13 +214,15 @@ public class AnnotationFile
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
- String key = String.valueOf(row.graphGroup);
+ Integer key = new Integer(row.graphGroup);
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+
}
else
{
+ graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
graphGroup.put(key, row.label);
}
}
@@ -376,21 +339,37 @@ public class AnnotationFile
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
+ if (graphLine.length()>0) {
+ text.append(graphLine.toString());
+ graphLine.setLength(0);
+ }
}
text.append(newline);
text.append(colours.toString());
- text.append(graphLine.toString());
if (graphGroup.size() > 0)
{
- Enumeration en = graphGroup.elements();
- while (en.hasMoreElements())
- {
+ SequenceI oldRefSeq = refSeq;
+ SequenceGroup oldRefGroup = refGroup;
+ for (Map.Entry combine_statement:graphGroup.entrySet())
+ {
+ Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey());
+
+ writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]);
+ refSeq = (SequenceI)seqRefAndGroup[0];
+
+ writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]);
+ refGroup = (SequenceGroup)seqRefAndGroup[1];
text.append("COMBINE\t");
- text.append(en.nextElement());
+ text.append(combine_statement.getValue());
text.append(newline);
}
+ writeSequence_Ref(refSeq, oldRefSeq);
+ refSeq = oldRefSeq;
+
+ writeGroup_Ref(refGroup, oldRefGroup);
+ refGroup = oldRefGroup;
}
text.append(rowprops.toString());
}
@@ -421,6 +400,62 @@ public class AnnotationFile
return text.toString();
}
+ private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+ {
+ if (next_refGroup == null)
+ {
+
+ if (refGroup != null)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ }
+ return true;
+ }
+ else
+ {
+ if (refGroup == null || refGroup != next_refGroup)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(next_refGroup.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+ {
+
+ if (next_refSeq==null)
+ {
+ if (refSeq != null)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ return true;
+ }
+ }
+ else
+ {
+ if (refSeq == null || refSeq != next_refSeq)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(next_refSeq.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
public void printGroups(List list)
{
SequenceI seqrep = null;
@@ -590,14 +625,13 @@ public class AnnotationFile
}
long nlinesread=0;
String lastread="";
+ private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
throws Exception
{
nlinesread = 0;
- /**
- * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
- */
- int combinecount = 0;
+ ArrayList