StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
- Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
+ Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
{
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);
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);
}
}
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
- if (graphLine.length()>0) {
+ if (graphLine.length() > 0)
+ {
text.append(graphLine.toString());
graphLine.setLength(0);
}
{
SequenceI oldRefSeq = refSeq;
SequenceGroup oldRefGroup = refGroup;
- for (Map.Entry<Integer, String> 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<Integer, String> 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;
}
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)
{
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)
{
{
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="";
- private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+
public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
throws Exception
{
boolean jvAnnotationFile = false;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0)
{
continue;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0
|| line.indexOf("JALVIEW_ANNOTATION") > -1
|| line.length() == 0)
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
- combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
+ combineAnnotation_calls.add(new Object[]
+ { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, refSeq, groupRef});
+ deferredAnnotation_calls.add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
{
addGroup(al, st);
- modified=true;
+ modified = true;
continue;
}
modified = true;
}
// Resolve the groupRefs
- Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
{
matched = true;
Vector rowset = (Vector) groupRefRows.get(groupRef);
- groupRefLookup.put(groupRef, theGroup);
+ groupRefLookup.put(groupRef, theGroup);
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
// group, or null
);
}
- }
+ }
// finally, combine all the annotation rows within each context.
/**
- * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
+ * number of combine statements in this annotation file. Used to create
+ * new groups for combined annotation graphs without disturbing existing
+ * ones
*/
int combinecount = 0;
- for (Object[] _combine_args:combineAnnotation_calls) {
- combineAnnotations(al,
+ for (Object[] _combine_args : combineAnnotation_calls)
+ {
+ combineAnnotations(al,
++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
- (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
- );
+ (_combine_args[2] == null) ? null : groupRefLookup
+ .get((String) _combine_args[2]) // the reference group,
+ // or null
+ );
}
}
return modified;
}
}
- void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void combineAnnotations(AlignmentI al, int combineCount,
+ StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
{
String group = st.nextToken();
// First make sure we are not overwriting the graphIndex
- int graphGroup=0;
+ int graphGroup = 0;
if (al.getAlignmentAnnotation() != null)
{
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-
- if (aa.graphGroup>graphGroup)
+
+ if (aa.graphGroup > graphGroup)
{
// try to number graphGroups in order of occurence.
- graphGroup=aa.graphGroup+1;
+ graphGroup = aa.graphGroup + 1;
}
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
- if (aa.graphGroup>-1)
+ if (aa.graphGroup > -1)
{
graphGroup = aa.graphGroup;
- } else {
+ }
+ else
+ {
if (graphGroup <= combineCount)
{
- graphGroup=combineCount+1;
+ graphGroup = combineCount + 1;
}
aa.graphGroup = graphGroup;
}
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
aa.graphGroup = graphGroup;
break;
}
}
- void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
+ SequenceGroup groupRef)
{
String group = st.nextToken();
AlignmentAnnotation annotation = null, alannot[] = al
{
for (int i = 0; i < alannot.length; i++)
{
- if (alannot[i].label.equalsIgnoreCase(group) && (seqRef==null || alannot[i].sequenceRef==seqRef) && (groupRef==null || alannot[i].groupRef==groupRef))
+ if (alannot[i].label.equalsIgnoreCase(group)
+ && (seqRef == null || alannot[i].sequenceRef == seqRef)
+ && (groupRef == null || alannot[i].groupRef == groupRef))
{
alannot[i].setThreshold(new GraphLine(value, label, colour));
}
git://source.jalview.org / jalview.git / blobdiff