+ public void printGroups(Vector sequenceGroups)\r
+ {\r
+ SequenceGroup sg;\r
+ SequenceI seqrep = null;\r
+ for (int i = 0; i < sequenceGroups.size(); i++)\r
+ {\r
+ sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
+ if (!sg.hasSeqrep())\r
+ {\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)\r
+ + "\t" + "-1\t");\r
+ seqrep = null;\r
+ }\r
+ else\r
+ {\r
+ seqrep = sg.getSeqrep();\r
+ text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (seqrep.findPosition(sg.getStartRes())) + "\t"\r
+ + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");\r
+ }\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ text.append(sg.getSequenceAt(s).getName() + "\t");\r
+ }\r
+\r
+ text.append("\nPROPERTIES\t" + sg.getName() + "\t");\r
+\r
+ if (sg.getDescription() != null)\r
+ {\r
+ text.append("description=" + sg.getDescription() + "\t");\r
+ }\r
+ if (sg.cs != null)\r
+ {\r
+ text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)\r
+ + "\t");\r
+ if (sg.cs.getThreshold() != 0)\r
+ {\r
+ text.append("pidThreshold=" + sg.cs.getThreshold());\r
+ }\r
+ if (sg.cs.conservationApplied())\r
+ {\r
+ text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");\r
+ }\r
+ }\r
+ text.append("outlineColour="\r
+ + jalview.util.Format.getHexString(sg.getOutlineColour())\r
+ + "\t");\r
+\r
+ text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
+ text.append("displayText=" + sg.getDisplayText() + "\t");\r
+ text.append("colourText=" + sg.getColourText() + "\t");\r
+ text.append("showUnconserved=" + sg.getShowunconserved() + "\t");\r
+ if (sg.textColour != java.awt.Color.black)\r
+ {\r
+ text.append("textCol1="\r
+ + jalview.util.Format.getHexString(sg.textColour) + "\t");\r
+ }\r
+ if (sg.textColour2 != java.awt.Color.white)\r
+ {\r
+ text.append("textCol2="\r
+ + jalview.util.Format.getHexString(sg.textColour2) + "\t");\r
+ }\r
+ if (sg.thresholdTextColour != 0)\r
+ {\r
+ text.append("textColThreshold=" + sg.thresholdTextColour + "\t");\r
+ }\r
+ if (sg.idColour != null)\r
+ {\r
+ text.append("idColour="\r
+ + jalview.util.Format.getHexString(sg.idColour) + "\t");\r
+ }\r
+ if (sg.isHidereps())\r
+ {\r
+ text.append("hide=true\t");\r
+ }\r
+ if (sg.isHideCols())\r
+ {\r
+ text.append("hidecols=true\t");\r
+ }\r
+ if (seqrep != null)\r
+ {\r
+ // terminate the last line and clear the sequence ref for the group\r
+ text.append("\nSEQUENCE_REF");\r
+ }\r
+ text.append("\n\n");\r
+\r
+ }\r
+ }\r