+ }\r
+\r
+ void addGroup(AlignmentI al, StringTokenizer st)\r
+ {\r
+ SequenceGroup sg = new SequenceGroup();\r
+ sg.setName(st.nextToken());\r
+ String rng = "";\r
+ try\r
+ {\r
+ rng = st.nextToken();\r
+ if (rng.length() > 0 && !rng.startsWith("*"))\r
+ {\r
+ sg.setStartRes(Integer.parseInt(rng) - 1);\r
+ }\r
+ else\r
+ {\r
+ sg.setStartRes(0);\r
+ }\r
+ rng = st.nextToken();\r
+ if (rng.length() > 0 && !rng.startsWith("*"))\r
+ {\r
+ sg.setEndRes(Integer.parseInt(rng) - 1);\r
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(al.getWidth() - 1);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"\r
+ + rng + "' - assuming alignment width for group.");\r
+ // assume group is full width\r
+ sg.setStartRes(0);\r
+ sg.setEndRes(al.getWidth() - 1);\r
+ }\r
+\r
+ String index = st.nextToken();\r
+ if (index.equals("-1"))\r
+ {\r
+ while (st.hasMoreElements())\r
+ {\r
+ sg.addSequence(al.findName(st.nextToken()), false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ StringTokenizer st2 = new StringTokenizer(index, ",");\r
+\r
+ while (st2.hasMoreTokens())\r
+ {\r
+ String tmp = st2.nextToken();\r
+ if (tmp.equals("*"))\r
+ {\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ sg.addSequence(al.getSequenceAt(i), false);\r
+ }\r
+ }\r
+ else if (tmp.indexOf("-") >= 0)\r
+ {\r
+ StringTokenizer st3 = new StringTokenizer(tmp, "-");\r
+\r
+ 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
+ if (refSeq != null)\r
+ {\r
+ sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\r
+ sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);\r
+ sg.setSeqrep(refSeq);\r
+ }\r
+\r
+ if (sg.getSize() > 0)\r
+ {\r
+ al.addGroup(sg);\r
+ }\r
+ }\r
+\r
+ void addRowProperties(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String label = st.nextToken(), keyValue, key, value;\r
+ boolean scaletofit = false, centerlab = false, showalllabs = false;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ if (key.equalsIgnoreCase("scaletofit"))\r
+ {\r
+ scaletofit = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("showalllabs"))\r
+ {\r
+ showalllabs = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("centrelabs"))\r
+ {\r
+ centerlab = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation();\r
+ if (alr != null)\r
+ {\r
+ for (int i = 0; i < alr.length; i++)\r
+ {\r
+ if (alr[i].label.equalsIgnoreCase(label))\r
+ {\r
+ alr[i].centreColLabels = centerlab;\r
+ alr[i].scaleColLabel = scaletofit;\r
+ alr[i].showAllColLabels = showalllabs;\r
+ }\r
+ }\r
+ }\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, sg.getSequences(null),\r
+ sg.getStartRes(), sg.getEndRes() + 1);\r