/*\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
public class SequenceGroup\r
{\r
String groupName;\r
+ String description;\r
Conservation conserve;\r
Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
+ boolean displayBoxes = true;\r
+ boolean displayText = true;\r
+ boolean colourText = true;\r
private Vector sequences = new Vector();\r
int width = -1;\r
\r
int startRes = 0;\r
int endRes = 0;\r
Color outlineColour = Color.black;\r
+ public int thresholdTextColour = 0;\r
+ public Color textColour = Color.black;\r
+ public Color textColour2 = Color.white;\r
+\r
\r
/**\r
* Creates a new SequenceGroup object.\r
*/\r
public SequenceGroup()\r
{\r
- groupName = "Group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
+ groupName = "JGroup:"+this.hashCode();\r
}\r
\r
/**\r
recalcConservation();\r
}\r
\r
- /**\r
- * Creates a new SequenceGroup object.\r
- *\r
- * @param groupName DOCUMENT ME!\r
- * @param scheme DOCUMENT ME!\r
- * @param displayBoxes DOCUMENT ME!\r
- * @param displayText DOCUMENT ME!\r
- * @param colourText DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- */\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText, boolean colourText,\r
- int start, int end)\r
- {\r
- this.groupName = groupName;\r
- this.displayBoxes = displayBoxes;\r
- this.displayText = displayText;\r
- this.colourText = colourText;\r
- this.cs = scheme;\r
- startRes = start;\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
- char ch;\r
- int sres, eres;\r
\r
for (int i = 0; i < iSize; i++)\r
{\r
SequenceI seq = inorder[i];\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- sres = seq.findPosition(startRes);\r
-\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- eres = 0;\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
seqs[i] = new Sequence(seq.getName(),\r
seq.getSequence(startRes, endRes + 1),\r
- sres,\r
- eres);\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
\r
}\r
\r
- public Vector getSequences(boolean includeHidden)\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(Hashtable hiddenReps)\r
{\r
- if(!includeHidden)\r
+ if(hiddenReps == null)\r
return sequences;\r
else\r
{\r
Vector allSequences = new Vector();\r
- SequenceI seq;\r
+ SequenceI seq, seq2;\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
+ if (hiddenReps.containsKey(seq) )\r
{\r
- for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+ SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);\r
+ for (int h = 0; h < hsg.getSize(); h++)\r
{\r
- allSequences.addElement(\r
- seq.getHiddenSequences().getSequenceAt(h)\r
- );\r
+ seq2 = hsg.getSequenceAt(h);\r
+ if (seq2 != seq\r
+ && !allSequences.contains(seq2))\r
+ allSequences.addElement(seq2);\r
}\r
}\r
}\r
}\r
}\r
\r
+ public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)\r
+ {\r
+ Vector tmp = getSequences(hiddenReps);\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
return groupName;\r
}\r
\r
+ public String getDescription()\r
+ {\r
+ return description;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
groupName = name;\r
}\r
\r
+ public void setDescription(String desc)\r
+ {\r
+ description = desc;\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
try\r
{\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
{\r
Conservation c = new Conservation(groupName,\r
ResidueProperties.propHash, 3, sequences,\r
- 0, getWidth());\r
+ startRes, endRes+1);\r
c.calculate();\r
c.verdict(false, 25);\r
\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getSize(boolean includeHidden)\r
+ public int getSize()\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