/*\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
+ * 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.analysis.*;\r
\r
-import jalview.datamodel.*;\r
-\r
import jalview.schemes.*;\r
\r
import java.awt.*;\r
\r
-import java.util.Vector;\r
+import java.util.*;\r
\r
\r
-public class SequenceGroup {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceGroup\r
+{\r
String groupName;\r
Conservation conserve;\r
Vector aaFrequency;\r
boolean displayBoxes;\r
boolean displayText;\r
boolean colourText;\r
+\r
+ /** DOCUMENT ME!! */\r
public 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
\r
- public SequenceGroup() {\r
+ /**\r
+ * Creates a new SequenceGroup object.\r
+ */\r
+ public SequenceGroup()\r
+ {\r
groupName = "Group";\r
this.displayBoxes = true;\r
this.displayText = true;\r
cs = null;\r
}\r
\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, boolean displayText,\r
+ boolean colourText, 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
+ /**\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
+ 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
+ * 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
- if (startRes >= col) {\r
+ if (startRes >= col)\r
+ {\r
startRes = startRes - col;\r
}\r
\r
- if (endRes >= col) {\r
+ if (endRes >= col)\r
+ {\r
endRes = endRes - col;\r
\r
- if (startRes > endRes) {\r
+ if (startRes > endRes)\r
+ {\r
startRes = 0;\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
// must delete this group!!\r
return false;\r
}\r
return true;\r
}\r
\r
- public boolean adjustForRemoveRight(int col) {\r
- if (startRes > col) {\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
+ {\r
// delete this group\r
return false;\r
}\r
\r
- if (endRes >= col) {\r
+ if (endRes >= col)\r
+ {\r
endRes = col;\r
}\r
\r
return true;\r
}\r
\r
- public String getName() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
return groupName;\r
}\r
\r
- public void setName(String name) {\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 Conservation getConservation() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Conservation getConservation()\r
+ {\r
return conserve;\r
}\r
\r
- public void setConservation(Conservation c) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setConservation(Conservation c)\r
+ {\r
conserve = c;\r
}\r
\r
- public void addSequence(SequenceI s) {\r
- if (!sequences.contains(s)) {\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
+ {\r
sequences.addElement(s);\r
}\r
\r
- if (cs != null) {\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
- }\r
-\r
- if (cs instanceof ConservationColourScheme) {\r
+ if (recalc)\r
+ {\r
recalcConservation();\r
}\r
}\r
\r
- void recalcConservation() {\r
- Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
- c.calculate();\r
- c.verdict(false, 25);\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void recalcConservation()\r
+ {\r
+ if(cs == null)\r
+ return;\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.conservationApplied())\r
+ {\r
+ Conservation c = new Conservation(groupName,\r
+ ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- ccs.conserve = c;\r
+ cs.setConservation(c);\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme) cs).resetClustalX(sequences,\r
+ getWidth());\r
+ }\r
+ }\r
}\r
\r
- public void addOrRemove(SequenceI s) {\r
- if (sequences.contains(s)) {\r
- deleteSequence(s);\r
- } else {\r
- addSequence(s);\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
+ deleteSequence(s, recalc);\r
+ }\r
+ else\r
+ {\r
+ addSequence(s, recalc);\r
}\r
}\r
\r
- public void deleteSequence(SequenceI s) {\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
\r
- if (cs != null) {\r
- cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
- }\r
-\r
- if (cs instanceof ConservationColourScheme) {\r
+ if (recalc)\r
+ {\r
recalcConservation();\r
}\r
}\r
\r
- public int getStartRes() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public void setStartRes(int i) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void setStartRes(int i)\r
+ {\r
startRes = i;\r
}\r
\r
- public void setEndRes(int i) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void setEndRes(int i)\r
+ {\r
endRes = i;\r
}\r
\r
- public int getSize() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getSize()\r
+ {\r
return sequences.size();\r
}\r
\r
- public SequenceI getSequenceAt(int i) {\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
- public void setColourText(boolean state) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setColourText(boolean state)\r
+ {\r
colourText = state;\r
}\r
\r
- public boolean getColourText() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getColourText()\r
+ {\r
return colourText;\r
}\r
\r
- public void setDisplayText(boolean state) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setDisplayText(boolean state)\r
+ {\r
displayText = state;\r
}\r
\r
- public boolean getDisplayText() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getDisplayText()\r
+ {\r
return displayText;\r
}\r
\r
- public void setDisplayBoxes(boolean state) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param state DOCUMENT ME!\r
+ */\r
+ public void setDisplayBoxes(boolean state)\r
+ {\r
displayBoxes = state;\r
}\r
\r
- public boolean getDisplayBoxes() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getDisplayBoxes()\r
+ {\r
return displayBoxes;\r
}\r
\r
- public int getWidth() {\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
- if (sequences.size() > 0) {\r
+ if (sequences.size() > 0)\r
+ {\r
width = ((SequenceI) sequences.elementAt(0)).getLength();\r
}\r
\r
- for (int i = 1; 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
+ if (seq.getLength() > width)\r
+ {\r
width = seq.getLength();\r
}\r
}\r
return width;\r
}\r
\r
- public void setOutlineColour(Color c) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ */\r
+ public void setOutlineColour(Color c)\r
+ {\r
outlineColour = c;\r
}\r
\r
- public Color getOutlineColour() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Color getOutlineColour()\r
+ {\r
return outlineColour;\r
}\r
\r
* @param al Alignment\r
* @return SequenceI[]\r
*/\r
- public SequenceI[] getSequencesInOrder(Alignment al) {\r
- int sz;\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 = sequences.size()];\r
+ SequenceI[] seqs = new SequenceI[sz];\r
\r
- for (int i = 0; i < sz; i++) {\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
int index = 0;\r
\r
- for (int i = 0; i < sz; i++) {\r
- SequenceI seq = null;\r
-\r
- while (seq == null) {\r
- if (orderedSeqs.containsKey(index + "")) {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- } else {\r
- index++;\r
- }\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ if (orderedSeqs.containsKey(i + ""))\r
+ {\r
+ seqs[index++] = (SequenceI) orderedSeqs.get(i + "");\r
}\r
-\r
- seqs[index] = seq;\r
}\r
\r
return seqs;\r
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