/*\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) 2007 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
*/\r
package jalview.datamodel;\r
\r
-import jalview.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.schemes.*;\r
+import java.util.*;\r
\r
import java.awt.*;\r
\r
-import java.util.Vector;\r
+import jalview.analysis.*;\r
+import jalview.schemes.*;\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\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
- public Vector sequences = new Vector();\r
+ boolean displayBoxes = true;\r
+ boolean displayText = true;\r
+ boolean colourText = true;\r
+ private Vector sequences = new Vector();\r
int width = -1;\r
+\r
+ /** DOCUMENT ME!! */\r
public ColourSchemeI cs;\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
+ * 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
- public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start, int end)\r
+ /**\r
+ * Creates a new SequenceGroup object.\r
+ *\r
+ * @param sequences DOCUMENT ME!\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(Vector sequences, String groupName,\r
+ ColourSchemeI scheme, boolean displayBoxes,\r
+ boolean displayText,\r
+ boolean colourText, int start, int end)\r
{\r
this.sequences = sequences;\r
this.groupName = groupName;\r
recalcConservation();\r
}\r
\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start, int end)\r
+ public SequenceI[] getSelectionAsNewSequences(AlignmentI align)\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
+ int iSize = sequences.size();\r
+ SequenceI[] seqs = new SequenceI[iSize];\r
+ SequenceI[] inorder = getSequencesInOrder(align);\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
+ {\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+ }\r
+\r
+ if (seq.getAnnotation() != null)\r
+ {\r
+ for (int a = 0; a < seq.getAnnotation().length; a++)\r
+ {\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\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(Hashtable hiddenReps)\r
+ {\r
+ if (hiddenReps == null)\r
+ {\r
+ return sequences;\r
+ }\r
+ else\r
+ {\r
+ Vector allSequences = new Vector();\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 (hiddenReps.containsKey(seq))\r
+ {\r
+ SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);\r
+ for (int h = 0; h < hsg.getSize(); h++)\r
+ {\r
+ seq2 = hsg.getSequenceAt(h);\r
+ if (seq2 != seq\r
+ && !allSequences.contains(seq2))\r
+ {\r
+ allSequences.addElement(seq2);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ return allSequences;\r
+ }\r
+ }\r
+\r
+ public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)\r
+ {\r
+ Vector tmp = getSequences(hiddenReps);\r
+ if (tmp == null)\r
+ {\r
+ return null;\r
+ }\r
+ SequenceI[] result = new SequenceI[tmp.size()];\r
+ for (int i = 0; i < result.length; i++)\r
+ {\r
+ result[i] = (SequenceI) tmp.elementAt(i);\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param col DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean adjustForRemoveLeft(int col)\r
{\r
// return value is true if the group still exists\r
return true;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param col DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean adjustForRemoveRight(int col)\r
{\r
if (startRes > col)\r
return true;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public String getName()\r
{\r
return groupName;\r
}\r
\r
+ public String getDescription()\r
+ {\r
+ return description;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ */\r
public void setName(String name)\r
{\r
groupName = name;\r
}\r
\r
+ public void setDescription(String desc)\r
+ {\r
+ description = desc;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public Conservation getConservation()\r
{\r
return conserve;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
public void setConservation(Conservation c)\r
{\r
conserve = c;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\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
- if(recalc)\r
+ if (recalc)\r
+ {\r
recalcConservation();\r
+ }\r
}\r
\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
public void recalcConservation()\r
{\r
- System.out.println("sg recalc");\r
- if (cs != null)\r
+ if (cs == null)\r
{\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ return;\r
}\r
\r
- if (cs instanceof ClustalxColourScheme)\r
+ try\r
{\r
- ( (ClustalxColourScheme) cs).resetClustalX(sequences,getWidth());\r
- }\r
+ cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));\r
\r
-\r
- if ( cs instanceof ConservationColourScheme)\r
- {\r
- Conservation c = new Conservation(groupName,\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
- if (ccs.cs instanceof ClustalxColourScheme)\r
+ if (cs instanceof ClustalxColourScheme)\r
{\r
- ( (ClustalxColourScheme) ccs.cs).resetClustalX(sequences, getWidth());\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
}\r
\r
+ if (cs.conservationApplied())\r
+ {\r
+ Conservation c = new Conservation(groupName,\r
+ ResidueProperties.propHash, 3,\r
+ sequences,\r
+ startRes, endRes + 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
+ cs.setConservation(c);\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\r
+ */\r
public void addOrRemove(SequenceI s, boolean recalc)\r
{\r
if (sequences.contains(s))\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param recalc DOCUMENT ME!\r
+ */\r
public void deleteSequence(SequenceI s, boolean recalc)\r
{\r
sequences.removeElement(s);\r
- if(recalc)\r
+\r
+ if (recalc)\r
+ {\r
recalcConservation();\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getStartRes()\r
{\r
return startRes;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getEndRes()\r
{\r
return endRes;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
public void setStartRes(int i)\r
{\r
startRes = i;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
public void setEndRes(int i)\r
{\r
endRes = i;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getSize()\r
{\r
return sequences.size();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public SequenceI getSequenceAt(int i)\r
{\r
return (SequenceI) sequences.elementAt(i);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
public void setColourText(boolean state)\r
{\r
colourText = state;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean getColourText()\r
{\r
return colourText;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
public void setDisplayText(boolean state)\r
{\r
displayText = state;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean getDisplayText()\r
{\r
return displayText;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
public void setDisplayBoxes(boolean state)\r
{\r
displayBoxes = state;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public boolean getDisplayBoxes()\r
{\r
return displayBoxes;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public int getWidth()\r
{\r
// MC This needs to get reset when characters are inserted and deleted\r
return width;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
public void setOutlineColour(Color c)\r
{\r
outlineColour = c;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public Color getOutlineColour()\r
{\r
return outlineColour;\r
* @param al Alignment\r
* @return SequenceI[]\r
*/\r
- public SequenceI[] getSequencesInOrder(Alignment al)\r
+ public SequenceI[] getSequencesInOrder(AlignmentI al)\r
{\r
- int sz;\r
- java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
- SequenceI[] seqs = new SequenceI[sz = sequences.size()];\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 < sz; i++)\r
+ for (int i = 0; i < alHeight && index < sSize; i++)\r
{\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
+ if (sequences.contains(al.getSequenceAt(i)))\r
{\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
+ seqs[index++] = al.getSequenceAt(i);\r
}\r
-\r
- seqs[index] = seq;\r
}\r
\r
return seqs;\r
git://source.jalview.org / jalview.git / blobdiff