X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=9809fa9a0223f0bd3b030faad72e1bd963d6c6e5;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=bcac5c76fdc8fb7555591f5ec9f73d715578a451;hpb=5b29190f1ea9500d3ad9f690ffb359f6aab17b80;p=jalview.git diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java index bcac5c7..9809fa9 100644 --- a/src/jalview/schemes/RNAHelicesColourChooser.java +++ b/src/jalview/schemes/RNAHelicesColourChooser.java @@ -1,38 +1,42 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; -import java.util.*; -import java.awt.event.*; - import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; + +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; /** * Helps generate the colors for RNA secondary structure. Future: add option to * change colors based on covariation. * * @author Lauren Michelle Lui - * + * @deprecated this seems to be unfinished - just use RNAHelicesColour */ +@Deprecated public class RNAHelicesColourChooser { @@ -42,9 +46,9 @@ public class RNAHelicesColourChooser ColourSchemeI oldcs; - Hashtable oldgroupColours; + Map oldgroupColours; - jalview.datamodel.AlignmentAnnotation currentAnnotation; + AlignmentAnnotation currentAnnotation; boolean adjusting = false; @@ -54,40 +58,40 @@ public class RNAHelicesColourChooser oldcs = av.getGlobalColourScheme(); if (av.getAlignment().getGroups() != null) { - oldgroupColours = new Hashtable(); + oldgroupColours = new Hashtable<>(); for (SequenceGroup sg : ap.getAlignment().getGroups()) { - if (sg.cs != null) + if (sg.getColourScheme() != null) { - oldgroupColours.put(sg, sg.cs); + oldgroupColours.put(sg, sg.getColourScheme()); } } } this.av = av; this.ap = ap; - if (oldcs instanceof RNAHelicesColour) - { - RNAHelicesColour rhc = (RNAHelicesColour) oldcs; - - } - adjusting = true; - Vector list = new Vector(); + Vector list = new Vector<>(); int index = 1; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + if (anns != null) { - String label = av.getAlignment().getAlignmentAnnotation()[i].label; - if (!list.contains(label)) - list.addElement(label); - else - list.addElement(label + "_" + (index++)); + for (int i = 0; i < anns.length; i++) + { + String label = anns[i].label; + if (!list.contains(label)) + { + list.addElement(label); + } + else + { + list.addElement(label + "_" + (index++)); + } + } } adjusting = false; - changeColour(); - } void changeColour() @@ -97,44 +101,10 @@ public class RNAHelicesColourChooser { return; } - RNAHelicesColour rhc = null; - - rhc = new RNAHelicesColour(av.getAlignment()); + RNAHelicesColour rhc = new RNAHelicesColour(av.getAlignment()); av.setGlobalColourScheme(rhc); - if (av.getAlignment().getGroups() != null) - { - for (SequenceGroup sg : ap.getAlignment().getGroups()) - { - if (sg.cs == null) - { - continue; - } - - sg.cs = new RNAHelicesColour(sg); - - } - } - - ap.paintAlignment(false); - } - - void reset() - { - av.setGlobalColourScheme(oldcs); - if (av.getAlignment().getGroups() != null) - { - for (SequenceGroup sg : ap.getAlignment().getGroups()) - { - sg.cs = (ColourSchemeI) oldgroupColours.get(sg); - } - } + ap.paintAlignment(true, true); } - - public void annotations_actionPerformed(ActionEvent e) - { - changeColour(); - } - }