{\r
public SequenceI sequenceRef;\r
\r
- /** This annotation is the original loaded annotation\r
- * without any gaps. It is necessary to adjust the annotation\r
- * if sequences are updated */\r
- public AlignmentAnnotation datasetAnnotation;\r
-\r
/** DOCUMENT ME!! */\r
public String label;\r
\r
/** DOCUMENT ME!! */\r
public Annotation[] annotations;\r
\r
+ public java.util.Hashtable sequenceMapping;\r
\r
/** DOCUMENT ME!! */\r
public float graphMin;\r
this.annotations = annotations;\r
graph = graphType;\r
\r
+ boolean drawValues = true;\r
+\r
if (min == max)\r
{\r
min = 999999999;\r
continue;\r
}\r
\r
+ if(drawValues && annotations[i].displayCharacter.length() > 1 )\r
+ {\r
+ drawValues = false;\r
+ }\r
+\r
if (annotations[i].value > max)\r
{\r
max = annotations[i].value;\r
\r
for (int i = 0; i < annotations.length; i++)\r
{\r
- if ((annotations[i] != null) &&\r
- ((annotations[i].secondaryStructure == 'H') ||\r
+ if (!hasIcons\r
+ && annotations[i] != null\r
+ && ((annotations[i].secondaryStructure == 'H') ||\r
(annotations[i].secondaryStructure == 'E')))\r
{\r
hasIcons = true;\r
}\r
\r
- if ((annotations[i] != null) &&\r
- (annotations[i].displayCharacter.length() > 0))\r
+ if (!hasText\r
+ && annotations[i]!=null\r
+ && annotations[i].displayCharacter.length() > 0)\r
{\r
hasText = true;\r
}\r
}\r
+\r
+ if(!drawValues && graphType!=NO_GRAPH)\r
+ {\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ if (annotations[i] != null)\r
+ annotations[i].displayCharacter = "";\r
+ }\r
+ }\r
}\r
\r
/**\r
return threshold;\r
}\r
\r
+ /**\r
+ * This\r
+ */\r
+ public void createSequenceMapping(SequenceI seqRef, int startRes)\r
+ {\r
+ if(seqRef == null)\r
+ return;\r
+\r
+ sequenceMapping = new java.util.Hashtable();\r
+\r
+ sequenceRef = seqRef;\r
+\r
+ if(startRes < sequenceRef.getStart())\r
+ startRes = sequenceRef.getStart();\r
+\r
+ int seqPos;\r
+\r
+ int fileOffset = 0;\r
+ if(startRes > sequenceRef.getStart())\r
+ {\r
+ fileOffset = startRes - sequenceRef.getStart();\r
+ }\r
+\r
+ for(int i = 0; i < annotations.length; i++)\r
+ {\r
+ seqPos = sequenceRef.findPosition(i + fileOffset);\r
+ if(seqPos<annotations.length)\r
+ {\r
+ if (annotations[i] != null)\r
+ {\r
+ sequenceMapping.put(new Integer(seqPos),\r
+ annotations[i]);\r
+ }\r
+ }\r
+ }\r
+\r
+ adjustForAlignment();\r
+\r
+ }\r
+\r
public void adjustForAlignment()\r
{\r
int a=0, aSize = sequenceRef.getLength();\r
\r
- int index = 0;\r
+ if(aSize == 0)\r
+ {\r
+ //Its been deleted\r
+ return;\r
+ }\r
+\r
+ int position;\r
Annotation[] temp = new Annotation[aSize];\r
+ Integer index;\r
\r
- for (a = 0; a < aSize; a++)\r
+ for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)\r
{\r
- if (!jalview.util.Comparison.isGap(sequenceRef.getCharAt(a)))\r
- {\r
- index = sequenceRef.findPosition(a);\r
- if(datasetAnnotation.annotations.length>index)\r
- temp[a] = datasetAnnotation.annotations[index];\r
- }\r
+ index = new Integer(a);\r
+ if(sequenceMapping.containsKey(index))\r
+ {\r
+ position = sequenceRef.findIndex(a)-1;\r
+\r
+ temp[position] = (Annotation)sequenceMapping.get(index);\r
+ }\r
}\r
\r
annotations = temp;\r