From 81bf67e64fade340738792bfbcd8b3a3efd3a010 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 15 Feb 2006 15:20:26 +0000 Subject: [PATCH] Removed SuperGroup --- src/jalview/appletgui/APopupMenu.java | 10 ------ src/jalview/datamodel/Alignment.java | 40 ------------------------ src/jalview/datamodel/AlignmentAnnotation.java | 17 +++------- src/jalview/datamodel/AlignmentI.java | 22 ------------- 4 files changed, 5 insertions(+), 84 deletions(-) diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index c90af98..a9a0e35 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -269,16 +269,6 @@ public class APopupMenu void refresh() { - SequenceGroup sg = getGroup(); - if(sg!=null) - { - SuperGroup superG = ap.av.alignment.getSuperGroup(sg); - - if (superG != null) - { - superG.setSuperGroupProperties(sg); - } - } ap.seqPanel.seqCanvas.repaint(); if(ap.overviewPanel!=null) ap.overviewPanel.updateOverviewImage(); diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 78aa015..b4e2b3f 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -390,47 +390,7 @@ public class Alignment implements AlignmentI return ret; } - /** - * DOCUMENT ME! - * - * @param sg DOCUMENT ME! - */ - public void addSuperGroup(SuperGroup sg) - { - superGroup.addElement(sg); - } - - /** - * DOCUMENT ME! - * - * @param sg DOCUMENT ME! - */ - public void removeSuperGroup(SuperGroup sg) - { - superGroup.removeElement(sg); - } - - /** - * DOCUMENT ME! - * - * @param sg DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SuperGroup getSuperGroup(SequenceGroup sg) - { - for (int i = 0; i < this.superGroup.size(); i++) - { - SuperGroup temp = (SuperGroup) superGroup.elementAt(i); - if (temp.sequenceGroups.contains(sg)) - { - return temp; - } - } - - return null; - } /** */ public void addGroup(SequenceGroup sg) diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index b93f178..6f22947 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -50,7 +50,7 @@ public class AlignmentAnnotation /** DOCUMENT ME!! */ public float graphMax; - public java.util.Vector graphLines; + public GraphLine threshold; // Graphical hints and tips @@ -233,21 +233,14 @@ public class AlignmentAnnotation return buffer.toString(); } - public void addGraphLine(GraphLine line) + public void setThreshold(GraphLine line) { - if(graphLines==null) - graphLines = new java.util.Vector(); - - graphLines.addElement(line); + threshold = line; } - public GraphLine getGraphLine(int index) + public GraphLine getTrheshold() { - if(graphLines!=null && index