X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=773633238ace37a835129e194cc4593d3fefc9cd;hb=ad5029edaf36ceaafb4e269f2e00b0e1e0d7ffc4;hp=b3a22df894f169bc408c3bef653c8eb86d691723;hpb=59c3078b53669a38f4e1c1158675691fe60349b3;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index b3a22df..7736332 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,19 +1,22 @@
/*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* 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 .
+ * 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;
@@ -131,8 +134,8 @@ public class AnnotationFile
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable graphGroup = new Hashtable();
- Hashtable graphGroup_refs = new Hashtable();
+ Hashtable graphGroup = new Hashtable();
+ Hashtable graphGroup_refs = new Hashtable();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
@@ -141,16 +144,19 @@ public class AnnotationFile
{
row = annotations[i];
- if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
+ if (!row.visible
+ && !row.hasScore()
+ && !(row.graphGroup > -1 && graphGroupSeen
+ .get(row.graphGroup)))
{
continue;
}
color = null;
oneColour = true;
-
+
// mark any sequence references for the row
- writeSequence_Ref(refSeq ,row.sequenceRef);
+ writeSequence_Ref(refSeq, row.sequenceRef);
refSeq = row.sequenceRef;
// mark any group references for the row
writeGroup_Ref(refGroup, row.groupRef);
@@ -217,11 +223,12 @@ public class AnnotationFile
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
-
+
}
else
{
- graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
+ graphGroup_refs.put(key, new Object[]
+ { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
@@ -338,32 +345,38 @@ 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)
{
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];
+ 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(combine_statement.getValue());
text.append(newline);
}
writeSequence_Ref(refSeq, oldRefSeq);
refSeq = oldRefSeq;
-
+
writeGroup_Ref(refGroup, oldRefGroup);
refGroup = oldRefGroup;
}
@@ -396,7 +409,8 @@ public class AnnotationFile
return text.toString();
}
- private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
{
if (next_refGroup == null)
{
@@ -421,13 +435,13 @@ public class AnnotationFile
return true;
}
}
- return false;
+ return false;
}
-
+
private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
{
- if (next_refSeq==null)
+ if (next_refSeq == null)
{
if (refSeq != null)
{
@@ -612,20 +626,28 @@ public class AnnotationFile
{
ex.printStackTrace();
System.out.println("Problem reading annotation file: " + ex);
- if (nlinesread>0) {
- System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ...");
+ if (nlinesread > 0)
+ {
+ System.out.println("Last read line " + nlinesread + ": '"
+ + lastread + "' (first 80 chars) ...");
}
return false;
}
return false;
}
- long nlinesread=0;
- String lastread="";
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+
public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
throws Exception
{
nlinesread = 0;
ArrayList