- String groupName;\r
- Conservation conserve;\r
- Vector aaFrequency;\r
- boolean displayBoxes;\r
- boolean displayText;\r
- boolean colourText;\r
- public Vector sequences = new Vector();\r
- int width = -1;\r
- public ColourSchemeI cs;\r
- int startRes = 0;\r
- int endRes = 0;\r
- Color outlineColour = Color.black;\r
-\r
- public SequenceGroup()\r
- {\r
- groupName = "Group";\r
- this.displayBoxes = true;\r
- this.displayText = true;\r
- this.colourText = false;\r
- cs = null;\r
- }\r
-\r
- public SequenceGroup(String groupName, ColourSchemeI scheme,\r
- boolean displayBoxes, boolean displayText,\r
- boolean colourText,\r
- int start,\r
- int end)\r
- {\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 boolean adjustForRemoveLeft(int col)\r
- {\r
- // return value is true if the group still exists\r
- if(startRes>=col)\r
- startRes = startRes - col;\r
- if(endRes>=col)\r
- {\r
- endRes = endRes - col;\r
- if(startRes>endRes)\r
- startRes = 0;\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
-\r
- if(startRes>col)\r
- {\r
- // delete this group\r
- return false;\r
- }\r
-\r
- if(endRes>=col)\r
- endRes = col;\r
-\r
- return true;\r
- }\r
-\r
-\r
- public String getName()\r
- {\r
- return groupName;\r
- }\r
-\r
- public void setName(String name)\r
- {\r
- groupName = name;\r
- }\r
-\r
- public Conservation getConservation()\r
- {\r
- return conserve;\r
- }\r
-\r
- public void setConservation(Conservation c)\r
- {\r
- conserve = c;\r
- }\r
-\r
- public void addSequence(SequenceI s)\r
- {\r
- if(!sequences.contains(s))\r
- sequences.addElement(s);\r
-\r
-\r
- if(cs!=null)\r
- cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );\r
-\r
- if(cs instanceof ConservationColourScheme)\r
- recalcConservation();\r
- }\r
-\r
- void recalcConservation()\r
- {\r
- Conservation c = new Conservation(groupName,\r
- ResidueProperties.propHash, 3,\r
- sequences, 0, getWidth());\r
- c.calculate();\r
- c.verdict(false, 25);\r
- ConservationColourScheme ccs = (ConservationColourScheme)cs;\r
- ccs.conserve = c;\r
- }\r
-\r
- public void addOrRemove(SequenceI s)\r
- {\r
- if(sequences.contains(s))\r
- deleteSequence(s);\r
- else\r
- addSequence(s);\r
- }\r
-\r
- public void deleteSequence(SequenceI s)\r
- {\r
- sequences.removeElement(s);\r
-\r
- if(cs!=null)\r
- cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );\r
-\r
- if(cs instanceof ConservationColourScheme)\r
- recalcConservation();\r
- }\r
-\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public void setStartRes(int i)\r
- {\r
- startRes = i;\r
- }\r
-\r
- public void setEndRes(int i)\r
- {\r
- endRes = i;\r
- }\r
-\r
- public int getSize()\r
- {\r
- return sequences.size();\r
- }\r
-\r
- public SequenceI getSequenceAt(int i)\r
- {\r
- return (SequenceI) sequences.elementAt(i);\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- colourText = state;\r
- }\r
-\r
- public boolean getColourText()\r
- {\r
- return colourText;\r
- }\r
-\r
- public void setDisplayText(boolean state)\r
- {\r
- displayText = state;\r
- }\r
-\r
- public boolean getDisplayText()\r
- {\r
- return displayText;\r
- }\r
-\r
- public void setDisplayBoxes(boolean state)\r
- {\r
- displayBoxes = state;\r
- }\r
-\r
- public boolean getDisplayBoxes()\r
- {\r
- return displayBoxes;\r
- }\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
- width = ((SequenceI) sequences.elementAt(0)).getLength();\r
- for (int i = 1; i < sequences.size(); i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.elementAt(i);\r
- if (seq.getLength() > width)\r
- width = seq.getLength();\r
- }\r
- return width;\r
- }\r
-\r
-\r
- public void setOutlineColour(Color c)\r
- {\r
- outlineColour = c;\r
- }\r
- public Color getOutlineColour()\r
- {\r
- return outlineColour;\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
- int sz;\r
- java.util.Hashtable orderedSeqs = new java.util.Hashtable();\r
- SequenceI[] seqs=new SequenceI[sz=sequences.size()];\r
- for(int i=0; i<sz; i++)\r
- {\r
- SequenceI seq = (SequenceI) sequences.get(i);\r
- int index = al.findIndex(seq);\r
- orderedSeqs.put(index+"", seq);\r
- }\r
-\r
- int index=0;\r
- for(int i=0; i<sz; i++) {\r
- SequenceI seq = null;\r
- while (seq == null)\r
+ String groupName;\r
+ Conservation conserve;\r
+ Vector aaFrequency;\r
+ boolean displayBoxes;\r
+ boolean displayText;\r
+ boolean colourText;\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
+\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
+ }\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
+ {\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
+\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