From 3d941a02a998676a12f8ff43fa98d9e1f4c27142 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 28 Nov 2006 16:48:11 +0000 Subject: [PATCH] CurrentColour must not be accessed by multiple sequence renderers --- src/jalview/schemes/AnnotationColourGradient.java | 4 ++-- src/jalview/schemes/Blosum62ColourScheme.java | 5 ++++- src/jalview/schemes/ClustalxColourScheme.java | 8 +++----- src/jalview/schemes/NucleotideColourScheme.java | 3 ++- src/jalview/schemes/PIDColourScheme.java | 4 ++-- src/jalview/schemes/ResidueColourScheme.java | 12 +++--------- src/jalview/schemes/ScoreColourScheme.java | 4 ++-- src/jalview/schemes/UserColourScheme.java | 3 ++- 8 files changed, 20 insertions(+), 23 deletions(-) diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java index c67eafc..8367cad 100755 --- a/src/jalview/schemes/AnnotationColourGradient.java +++ b/src/jalview/schemes/AnnotationColourGradient.java @@ -141,7 +141,7 @@ public class AnnotationColourGradient extends ResidueColourScheme */ public Color findColour(String n, int j) { - currentColour = Color.white; + Color currentColour = Color.white; if ((threshold == 0) || aboveThreshold(n, j)) { @@ -179,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; } diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java index ec5d4f1..d3b93bf 100755 --- a/src/jalview/schemes/Blosum62ColourScheme.java +++ b/src/jalview/schemes/Blosum62ColourScheme.java @@ -32,6 +32,7 @@ public class Blosum62ColourScheme public Color findColour(String s, int j) { + char res = s.charAt(0); if ('a' <= res && res <= 'z' ) { @@ -47,6 +48,8 @@ public class Blosum62ColourScheme return Color.white; } + Color currentColour; + if (!jalview.util.Comparison.isGap( res )) { String max = (String) consensus[j].get(AAFrequency.MAXRESIDUE); @@ -79,7 +82,7 @@ public class Blosum62ColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); } else { diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index 04610ef..ce30de8 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -247,12 +247,10 @@ public class ClustalxColourScheme public Color findColour(String s, int j) { - - if(cons2.length<=j) - return currentColour; + Color currentColour; - if ( (threshold != 0) && !aboveThreshold(s, j)) + if ( cons2.length<=j || (threshold != 0 && !aboveThreshold(s, j))) { return Color.white; } @@ -283,7 +281,7 @@ public class ClustalxColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; } diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index 6aaef7d..f36bcad 100755 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -60,6 +60,7 @@ public class NucleotideColourScheme extends ResidueColourScheme */ public Color findColour(String n, int j) { + Color currentColour; if ((threshold == 0) || aboveThreshold(n, j)) { try @@ -77,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; } diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java index 8061e67..b287384 100755 --- a/src/jalview/schemes/PIDColourScheme.java +++ b/src/jalview/schemes/PIDColourScheme.java @@ -56,7 +56,7 @@ public class PIDColourScheme return Color.white; } - currentColour = Color.white; + Color currentColour = Color.white; double sc = 0; @@ -83,7 +83,7 @@ public class PIDColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; } diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index 64fd62e..bf83665 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -52,12 +52,6 @@ public class ResidueColourScheme implements ColourSchemeI /** DOCUMENT ME!! */ int inc = 30; - /** - * The colour to be calculated, manipulated and returned - */ - Color currentColour = null; - - /** * Creates a new ResidueColourScheme object. @@ -90,7 +84,7 @@ public class ResidueColourScheme implements ColourSchemeI public Color findColour(String s, int j) { - + Color currentColour; int index = ResidueProperties.aaIndex[s.charAt(0)]; if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j)) @@ -103,7 +97,7 @@ public class ResidueColourScheme implements ColourSchemeI } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; @@ -227,7 +221,7 @@ public class ResidueColourScheme implements ColourSchemeI * @return DOCUMENT ME! */ - void applyConservation(int i) + void applyConservation(Color currentColour, int i) { if ((conservation[i] != '*') && (conservation[i] != '+')) diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java index 1f9116c..c9f7fc8 100755 --- a/src/jalview/schemes/ScoreColourScheme.java +++ b/src/jalview/schemes/ScoreColourScheme.java @@ -99,10 +99,10 @@ public class ScoreColourScheme extends ResidueColourScheme return Color.white; } - currentColour = colors[ ResidueProperties.aaIndex[c] ]; + Color currentColour = colors[ ResidueProperties.aaIndex[c] ]; if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; } diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 3349283..9d61279 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -188,6 +188,7 @@ public class UserColourScheme public Color findColour(String s, int j) { + Color currentColour; int index = ResidueProperties.aaIndex[s.charAt(0)]; if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j)) @@ -203,7 +204,7 @@ public class UserColourScheme } if(conservationColouring) - applyConservation(j); + applyConservation(currentColour, j); return currentColour; -- 1.7.10.2