+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.datamodel;\r
\r
-import jalview.schemes.*;\r
import jalview.analysis.*;\r
+\r
import jalview.datamodel.*;\r
-import java.util.Vector;\r
+\r
+import jalview.schemes.*;\r
+\r
import java.awt.*;\r
\r
+import java.util.Vector;\r
+\r
public class SequenceGroup\r
{\r
String groupName;\r
boolean displayBoxes;\r
boolean displayText;\r
boolean colourText;\r
- boolean aaFrequencyValid = false;\r
public Vector sequences = new Vector();\r
int width = -1;\r
public ColourSchemeI cs;\r
cs = null;\r
}\r
\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+ public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,\r
boolean displayBoxes, boolean displayText,\r
boolean colourText,\r
- int start,\r
- int end)\r
+ int start, int end)\r
{\r
+ this.sequences = sequences;\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
+ recalcConservation();\r
+ }\r
\r
+ public SequenceGroup(String groupName, ColourSchemeI scheme,\r
+ boolean displayBoxes, boolean displayText,\r
+ boolean colourText,\r
+ int start, int end)\r
+ {\r
this.groupName = groupName;\r
this.displayBoxes = displayBoxes;\r
this.displayText = displayText;\r
endRes = end;\r
}\r
\r
+ public boolean adjustForRemoveLeft(int col)\r
+ {\r
+ // return value is true if the group still exists\r
+ if (startRes >= col)\r
+ {\r
+ startRes = startRes - col;\r
+ }\r
+\r
+ if (endRes >= col)\r
+ {\r
+ endRes = endRes - col;\r
+\r
+ if (startRes > endRes)\r
+ {\r
+ startRes = 0;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // must delete this group!!\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+ public boolean adjustForRemoveRight(int col)\r
+ {\r
+ if (startRes > col)\r
+ {\r
+ // delete this group\r
+ return false;\r
+ }\r
+\r
+ if (endRes >= col)\r
+ {\r
+ endRes = col;\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
public String getName()\r
{\r
return groupName;\r
conserve = c;\r
}\r
\r
- public void addSequence(SequenceI s)\r
+ public void addSequence(SequenceI s, boolean recalc)\r
{\r
- if(!sequences.contains(s))\r
+ if (!sequences.contains(s))\r
sequences.addElement(s);\r
+\r
+ if(recalc)\r
+ recalcConservation();\r
}\r
\r
- public void addOrRemove(SequenceI s)\r
+\r
+ public void recalcConservation()\r
{\r
- if(sequences.contains(s))\r
- deleteSequence(s);\r
+ System.out.println("sg recalc");\r
+ if (cs != null)\r
+ {\r
+ cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
+ }\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).resetClustalX(sequences,getWidth());\r
+ }\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
+ {\r
+ ( (ClustalxColourScheme) ccs.cs).resetClustalX(sequences, getWidth());\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ public void addOrRemove(SequenceI s, boolean recalc)\r
+ {\r
+ if (sequences.contains(s))\r
+ {\r
+ deleteSequence(s, recalc);\r
+ }\r
else\r
- addSequence(s);\r
+ {\r
+ addSequence(s, recalc);\r
+ }\r
}\r
\r
- public void deleteSequence(SequenceI s)\r
+ public void deleteSequence(SequenceI s, boolean recalc)\r
{\r
sequences.removeElement(s);\r
+ if(recalc)\r
+ recalcConservation();\r
}\r
\r
-\r
public int getStartRes()\r
{\r
return startRes;\r
return displayBoxes;\r
}\r
\r
- public Vector getAAFrequency()\r
+ public int getWidth()\r
{\r
- if (aaFrequency == null || aaFrequencyValid == false)\r
+ // MC This needs to get reset when characters are inserted and deleted\r
+ if (sequences.size() > 0)\r
{\r
- aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());\r
- aaFrequencyValid = true;\r
+ width = ( (SequenceI) sequences.elementAt(0)).getLength();\r
}\r
- return aaFrequency;\r
- }\r
\r
- public int getWidth()\r
- {\r
- System.out.println("it is called");\r
- // MC This needs to get reset when characters are inserted and deleted\r
- for (int i = 0; i < sequences.size(); i++)\r
+ for (int i = 1; i < sequences.size(); i++)\r
{\r
SequenceI seq = (SequenceI) sequences.elementAt(i);\r
+\r
if (seq.getLength() > width)\r
+ {\r
width = seq.getLength();\r
+ }\r
}\r
+\r
return width;\r
}\r
\r
-\r
public void setOutlineColour(Color c)\r
{\r
outlineColour = c;\r
}\r
+\r
public Color getOutlineColour()\r
{\r
return outlineColour;\r
}\r
+\r
+ /**\r
+ *\r
+ * returns the sequences in the group ordered by the ordering given by al\r
+ *\r
+ * @param al Alignment\r
+ * @return SequenceI[]\r
+ */\r
+ public SequenceI[] getSequencesInOrder(Alignment al)\r
+ {\r
+ int sz;\r
+ java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
+ SequenceI[] seqs = new SequenceI[sz = sequences.size()];\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
+\r
+ int index = 0;\r
+\r
+ for (int i = 0; i < sz; i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\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
+ }\r
+\r
+ seqs[index] = seq;\r
+ }\r
+\r
+ return seqs;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff