+ int start = (Integer.parseInt(st3.nextToken()));\r
+ int end = (Integer.parseInt(st3.nextToken()));\r
+\r
+ if (end > start)\r
+ {\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ sg.addSequence(al.getSequenceAt(i - 1), false);\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+\r
+ if (refSeq != null)\r
+ {\r
+ sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\r
+ sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);\r
+ }\r
+\r
+ if (sg.getSize() > 0)\r
+ {\r
+ al.addGroup(sg);\r
+ }\r
+ }\r
+\r
+ void addProperties(AlignmentI al, StringTokenizer st)\r
+ {\r
+\r
+ //So far we have only added groups to the annotationHash,\r
+ //the idea is in the future properties can be added to\r
+ //alignments, other annotations etc\r
+ if (al.getGroups() == null)\r
+ {\r
+ return;\r
+ }\r
+ SequenceGroup sg = null;\r
+\r
+ String name = st.nextToken();\r
+\r
+ Vector groups = al.getGroups();\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ sg = (SequenceGroup) groups.elementAt(i);\r
+ if (sg.getName().equals(name))\r
+ {\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ sg = null;\r
+ }\r
+ }\r
+\r
+ if (sg != null)\r
+ {\r
+ String keyValue, key, value;\r
+ ColourSchemeI def = sg.cs;\r
+ sg.cs = null;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+\r
+ if (key.equalsIgnoreCase("description"))\r
+ {\r
+ sg.setDescription(value);\r
+ }\r
+ else if (key.equalsIgnoreCase("colour"))\r
+ {\r
+ sg.cs = ColourSchemeProperty.getColour(al, value);\r
+ }\r
+ else if (key.equalsIgnoreCase("pidThreshold"))\r
+ {\r
+ sg.cs.setThreshold(Integer.parseInt(value), true);\r
+\r
+ }\r
+ else if (key.equalsIgnoreCase("consThreshold"))\r
+ {\r
+ sg.cs.setConservationInc(Integer.parseInt(value));\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(null),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
+ sg.cs.setConservation(c);\r
+\r
+ }\r
+ else if (key.equalsIgnoreCase("outlineColour"))\r
+ {\r
+ sg.setOutlineColour(new UserColourScheme(value).findColour('A'));\r
+ }\r
+ else if (key.equalsIgnoreCase("displayBoxes"))\r
+ {\r
+ sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("displayText"))\r
+ {\r
+ sg.setDisplayText(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("colourText"))\r
+ {\r
+ sg.setColourText(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("textCol1"))\r
+ {\r
+ sg.textColour = new UserColourScheme(value).findColour('A');\r
+ }\r
+ else if (key.equalsIgnoreCase("textCol2"))\r
+ {\r
+ sg.textColour2 = new UserColourScheme(value).findColour('A');\r
+ }\r
+ else if (key.equalsIgnoreCase("textColThreshold"))\r
+ {\r
+ sg.thresholdTextColour = Integer.parseInt(value);\r
+ }\r
+ else if (key.equalsIgnoreCase("idColour"))\r
+ {\r
+ // consider warning if colour doesn't resolve to a real colour\r
+ sg.setIdColour((def = new UserColourScheme(value)).findColour('A'));\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ if (sg.cs==null)\r
+ {\r
+ sg.cs = def;\r
+ }\r
+ }\r
+ }\r
+\r
+ void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String token;\r
+ AlignmentAnnotation aa;\r
+ while(st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if(aa.sequenceRef==refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String keyValue, key, value;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ al.setProperty(key,value);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i=0; i<annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp>p)\r
+ {\r
+ sp.append(atos.substring(p, cp+1));\r
+ } else {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp+1;\r
+ } while (p>0);\r
+ }\r
+ return sp.toString();\r