/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
* \r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
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
String key = en.nextElement().toString();\r
text.append("\t" + key + "=" + properties.get(key));\r
}\r
+ // TODO: output alignment visualization settings here if required\r
\r
}\r
\r
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
text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
text.append("displayText=" + sg.getDisplayText() + "\t");\r
text.append("colourText=" + sg.getColourText() + "\t");\r
-\r
+ text.append("showUnconserved="+sg.getShowunconserved()+"\t");\r
if (sg.textColour != java.awt.Color.black)\r
{\r
text.append("textCol1="\r
}\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
token = st.nextToken();\r
if (token.equalsIgnoreCase("COLOUR"))\r
{\r
+ // TODO: use graduated colour def'n here too\r
colourAnnotations(al, st.nextToken(), st.nextToken());\r
continue;\r
}\r
if (refSeq != null)\r
{\r
annotation.belowAlignment = false;\r
+ // make a copy of refSeq so we can find other matches in the alignment\r
+ SequenceI referedSeq = refSeq;\r
do\r
{\r
// copy before we do any mapping business.\r
// TODO: verify that undo/redo with 1:many sequence associated\r
// annotations can be undone correctly\r
AlignmentAnnotation ann = new AlignmentAnnotation(annotation);\r
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
+ annotation.createSequenceMapping(referedSeq, refSeqIndex, false);\r
annotation.adjustForAlignment();\r
- refSeq.addAlignmentAnnotation(annotation);\r
+ referedSeq.addAlignmentAnnotation(annotation);\r
al.addAnnotation(annotation);\r
al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length\r
annotation = ann;\r
\r
} while (refSeqId != null\r
- && (refSeq = al.findName(refSeq, refSeqId, true)) != null);\r
+ && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);\r
}\r
else\r
{\r
\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
{\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
{\r
sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());\r
}\r
+ else if (key.equalsIgnoreCase("showUnconserved"))\r
+ {\r
+ sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+ }\r
else if (key.equalsIgnoreCase("displayText"))\r
{\r
sg.setDisplayText(Boolean.valueOf(value).booleanValue());\r
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