From 38291a0c2fb379a3680dd82dce86e5879869bc50 Mon Sep 17 00:00:00 2001 From: Renia Correya Date: Thu, 25 Jul 2024 10:17:22 +0100 Subject: [PATCH] JAL-4392 Print annotations Added colour by secondary structure conservation threshold to the output file --- src/jalview/io/AnnotationFile.java | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 7e4ee16..66c620b 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -569,6 +569,12 @@ public class AnnotationFile text.append("pidThreshold="); text.append(sg.cs.getThreshold()); } + if (sg.cs.isConsensusSecondaryStructureColouring()) + { + text.append("secondaryStructureConservationThreshold="); + text.append(sg.cs.getConsensusSecondaryStructureThreshold()); + text.append("\t"); + } if (sg.cs.conservationApplied()) { text.append("consThreshold="); @@ -1601,6 +1607,12 @@ public class AnnotationFile sg.cs.setThreshold(Integer.parseInt(value), true); } + else if(key.equalsIgnoreCase("secondaryStructureConservationThreshold")) + { + sg.cs.setConsensusSecondaryStructureThreshold(Integer.parseInt(value)); + sg.cs.setConsensusSecondaryStructureColouring(true); + + } else if (key.equalsIgnoreCase("consThreshold")) { sg.cs.setConservationInc(Integer.parseInt(value)); -- 1.7.10.2