/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
boolean displayBoxes;\r
boolean displayText;\r
boolean colourText;\r
-\r
- /** DOCUMENT ME!! */\r
- public Vector sequences = new Vector();\r
+ private Vector sequences = new Vector();\r
int width = -1;\r
\r
/** DOCUMENT ME!! */\r
endRes = end;\r
}\r
\r
+ public SequenceI [] getSelectionAsNewSequences(AlignmentI align)\r
+ {\r
+ int iSize = sequences.size();\r
+ SequenceI [] seqs = new SequenceI[iSize];\r
+ SequenceI [] inorder = getSequencesInOrder(align);\r
+\r
+\r
+ for (int i = 0; i < iSize; i++)\r
+ {\r
+ SequenceI seq = inorder[i];\r
+\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(startRes, endRes + 1),\r
+ seq.findPosition(startRes),\r
+ findEndRes(seq));\r
+\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ if (seq.getDatasetSequence() != null)\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+ if(seq.getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<seq.getAnnotation().length; a++)\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\r
+ }\r
+\r
+ return seqs;\r
+\r
+ }\r
+\r
+ /**\r
+ * If sequence ends in gaps, the end residue can\r
+ * be correctly calculated here\r
+ * @param seq SequenceI\r
+ * @return int\r
+ */\r
+ public int findEndRes(SequenceI seq)\r
+ {\r
+ int eres = 0;\r
+ char ch;\r
+\r
+ for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ eres++;\r
+ }\r
+ }\r
+\r
+ if (eres > 0)\r
+ {\r
+ eres += seq.getStart() - 1;\r
+ }\r
+\r
+ return eres;\r
+ }\r
+\r
+ public Vector getSequences(boolean includeHidden)\r
+ {\r
+ if(!includeHidden)\r
+ return sequences;\r
+ else\r
+ {\r
+ Vector allSequences = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq = (SequenceI) sequences.elementAt(i);\r
+ allSequences.addElement(seq);\r
+ if (seq.getHiddenSequences() != null)\r
+ {\r
+ for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+ {\r
+ allSequences.addElement(\r
+ seq.getHiddenSequences().getSequenceAt(h)\r
+ );\r
+ }\r
+ }\r
+ }\r
+\r
+ return allSequences;\r
+ }\r
+ }\r
+\r
+ public SequenceI[] getSequencesAsArray(boolean includeHidden)\r
+ {\r
+ Vector tmp = getSequences(includeHidden);\r
+ if(tmp==null)\r
+ return null;\r
+ SequenceI [] result = new SequenceI[tmp.size()];\r
+ for(int i=0; i<result.length; i++)\r
+ result[i] = (SequenceI)tmp.elementAt(i);\r
+\r
+ return result;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void addSequence(SequenceI s, boolean recalc)\r
{\r
- if (!sequences.contains(s))\r
+ if (s!=null && !sequences.contains(s))\r
{\r
sequences.addElement(s);\r
}\r
*/\r
public void recalcConservation()\r
{\r
- if (cs != null)\r
- {\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
- }\r
+ if(cs == null)\r
+ return;\r
\r
- if (cs instanceof ClustalxColourScheme)\r
+ try\r
{\r
- ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
- }\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
+ }\r
+\r
+ if (cs.conservationApplied())\r
+ {\r
Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+ ResidueProperties.propHash, 3, sequences,\r
+ 0, getWidth());\r
c.calculate();\r
c.verdict(false, 25);\r
\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- ccs.conserve = c;\r
+ cs.setConservation(c);\r
\r
- if (ccs.cs instanceof ClustalxColourScheme)\r
+ if (cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,\r
- getWidth());\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences,\r
+ getWidth());\r
}\r
+ }\r
+ }\r
+ catch (java.lang.OutOfMemoryError err)\r
+ {\r
+ System.out.println("Out of memory loading groups: " + err);\r
}\r
+\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getSize()\r
+ public int getSize(boolean includeHidden)\r
{\r
+ if(!includeHidden)\r
return sequences.size();\r
+ else\r
+ {\r
+ int total = sequences.size();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sequences.size(); i++)\r
+ {\r
+ seq = (SequenceI) sequences.elementAt(i);\r
+ if (seq.getHiddenSequences() != null)\r
+ {\r
+ total += seq.getHiddenSequences().getSize(false);\r
+ }\r
+ }\r
+ return total;\r
+ }\r
}\r
\r
/**\r
*/\r
public SequenceI[] getSequencesInOrder(AlignmentI al)\r
{\r
- int sz = sequences.size();\r
- java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
- SequenceI[] seqs = new SequenceI[sz];\r
+ int sSize = sequences.size();\r
+ int alHeight = al.getHeight();\r
\r
- for (int i = 0; i < sz; i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- int index = al.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
- }\r
+ SequenceI[] seqs = new SequenceI[sSize];\r
\r
int index = 0;\r
-\r
- for (int i = 0; i < al.getHeight(); i++)\r
+ for (int i = 0; i < alHeight && index<sSize; i++)\r
{\r
- if (orderedSeqs.containsKey(i + ""))\r
- {\r
- seqs[index++] = (SequenceI) orderedSeqs.get(i + "");\r
- }\r
+ if(sequences.contains( al.getSequenceAt(i) ) )\r
+ seqs[index++] = al.getSequenceAt(i);\r
}\r
\r
return seqs;\r
git://source.jalview.org / jalview.git / blobdiff