X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=fc92cd96b2f400fcb0cc4739d640f6b28df25877;hb=36067eda8f713ab855b839fd4cc9af5cf36854a4;hp=a9815492748a8e1c51c541d5bcfcaddcdea299e6;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index a981549..fc92cd9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,148 +1,155 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.schemes;
-
-public class ColourSchemeProperty
-{
- public static final int CLUSTAL = 0;
- public static final int BLOSUM = 1;
- public static final int PID = 2;
- public static final int ZAPPO = 3;
- public static final int HYDROPHOBIC=4;
- public static final int HELIX=5;
- public static final int STRAND=6;
- public static final int TURN = 7;
- public static final int BURIED = 8;
- public static final int NUCLEOTIDE = 9;
- public static final int USER_DEFINED = 10;
- public static final int NONE = 11;
-
- public static int getColourIndexFromName(String name)
- {
- int ret=11;
- if(name.equalsIgnoreCase("Clustal"))
- ret = CLUSTAL;
- else if(name.equalsIgnoreCase("Blosum62"))
- ret = BLOSUM;
- else if(name.equalsIgnoreCase("% Identity"))
- ret = PID;
- else if(name.equalsIgnoreCase("Zappo"))
- ret = ZAPPO;
- else if(name.equalsIgnoreCase("Hydrophobic"))
- ret = HYDROPHOBIC;
- else if(name.equalsIgnoreCase("Helix Propensity"))
- ret = HELIX;
- else if(name.equalsIgnoreCase("Strand Propensity"))
- ret = STRAND;
- else if(name.equalsIgnoreCase("Turn Propensity"))
- ret = TURN;
- else if(name.equalsIgnoreCase("Buried Index"))
- ret = BURIED;
- else if(name.equalsIgnoreCase("Nucleotide"))
- ret = NUCLEOTIDE;
- else if(name.equalsIgnoreCase("User Defined"))
- ret = USER_DEFINED;
-
- return ret;
- }
-
- public static String getColourName(ColourSchemeI cs)
- {
- if(cs instanceof ConservationColourScheme)
- cs = ((ConservationColourScheme)cs).cs;
-
-
- int index = 11;
- if(cs instanceof ClustalxColourScheme)
- index = CLUSTAL;
- else if(cs instanceof Blosum62ColourScheme)
- index = BLOSUM;
- else if(cs instanceof PIDColourScheme)
- index = PID;
- else if(cs instanceof ZappoColourScheme)
- index = ZAPPO;
- else if(cs instanceof HydrophobicColourScheme)
- index = HYDROPHOBIC;
- else if(cs instanceof HelixColourScheme)
- index = HELIX;
- else if(cs instanceof StrandColourScheme)
- index = STRAND;
- else if(cs instanceof TurnColourScheme)
- index = TURN;
- else if(cs instanceof BuriedColourScheme)
- index = BURIED;
- else if(cs instanceof NucleotideColourScheme)
- index = NUCLEOTIDE;
- else if(cs instanceof UserColourScheme)
- index = USER_DEFINED;
-
- return getColourName(index);
- }
-
- public static String getColourName(int index)
- {
- String ret=null;
- switch(index)
- {
- case CLUSTAL: ret = "Clustal"; break;
- case BLOSUM: ret = "Blosum62"; break;
- case PID: ret = "% Identity"; break;
- case ZAPPO: ret = "Zappo"; break;
- case HYDROPHOBIC: ret="Hydrophobic";break;
- case HELIX: ret="Helix Propensity";break;
- case STRAND: ret="Strand Propensity";break;
- case TURN: ret="Turn Propensity";break;
- case BURIED: ret="Buried Index";break;
- case NUCLEOTIDE:ret="Nucleotide"; break;
- case USER_DEFINED:ret="User Defined";break;
- default: ret = "None"; break;
- }
- return ret;
- }
-
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
- {
- return getColour(al, getColourIndexFromName(name));
- }
-
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
- {
- ColourSchemeI cs = null;
- switch(index)
- {
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
- case BLOSUM: cs = new Blosum62ColourScheme(); break;
- case PID: cs = new PIDColourScheme(); break;
- case ZAPPO: cs = new ZappoColourScheme(); break;
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
- case HELIX: cs = new HelixColourScheme(); break;
- case STRAND: cs = new StrandColourScheme(); break;
- case TURN: cs = new TurnColourScheme(); break;
- case BURIED: cs = new BuriedColourScheme(); break;
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
- case USER_DEFINED: cs = new UserColourScheme(null);
- break;
-
- default: break;
- }
-
- return cs;
- }
-}
+/*
+ * 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.
+ *
+ * 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