From ac33424148b2a4de29b3ca43f941162e8ba0384c Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 29 Jun 2012 16:18:41 +0100 Subject: [PATCH] JAL-1065 JAL-1066 allow different lookup tables for nucleotide or amino acid colourschemes --- src/jalview/schemes/BuriedColourScheme.java | 2 +- src/jalview/schemes/HelixColourScheme.java | 2 +- src/jalview/schemes/HydrophobicColourScheme.java | 2 +- src/jalview/schemes/NucleotideColourScheme.java | 2 +- .../schemes/PurinePyrimidineColourScheme.java | 2 +- src/jalview/schemes/ResidueColourScheme.java | 27 +++++++++++++------- src/jalview/schemes/ScoreColourScheme.java | 4 +-- src/jalview/schemes/StrandColourScheme.java | 2 +- src/jalview/schemes/TaylorColourScheme.java | 2 +- src/jalview/schemes/TurnColourScheme.java | 2 +- src/jalview/schemes/ZappoColourScheme.java | 2 +- 11 files changed, 29 insertions(+), 20 deletions(-) diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java index 6ccdef5..7ac6546 100755 --- a/src/jalview/schemes/BuriedColourScheme.java +++ b/src/jalview/schemes/BuriedColourScheme.java @@ -32,7 +32,7 @@ public class BuriedColourScheme extends ScoreColourScheme */ public BuriedColourScheme() { - super(ResidueProperties.buried, ResidueProperties.buriedmin, + super(ResidueProperties.aaIndex, ResidueProperties.buried, ResidueProperties.buriedmin, ResidueProperties.buriedmax); } diff --git a/src/jalview/schemes/HelixColourScheme.java b/src/jalview/schemes/HelixColourScheme.java index ca2bb61..3683b80 100755 --- a/src/jalview/schemes/HelixColourScheme.java +++ b/src/jalview/schemes/HelixColourScheme.java @@ -23,7 +23,7 @@ public class HelixColourScheme extends ScoreColourScheme { public HelixColourScheme() { - super(ResidueProperties.helix, ResidueProperties.helixmin, + super(ResidueProperties.aaIndex, ResidueProperties.helix, ResidueProperties.helixmin, ResidueProperties.helixmax); } diff --git a/src/jalview/schemes/HydrophobicColourScheme.java b/src/jalview/schemes/HydrophobicColourScheme.java index 4dd05c1..0cb365f 100755 --- a/src/jalview/schemes/HydrophobicColourScheme.java +++ b/src/jalview/schemes/HydrophobicColourScheme.java @@ -32,7 +32,7 @@ public class HydrophobicColourScheme extends ScoreColourScheme */ public HydrophobicColourScheme() { - super(ResidueProperties.hyd, ResidueProperties.hydmin, + super(ResidueProperties.aaIndex, ResidueProperties.hyd, ResidueProperties.hydmin, ResidueProperties.hydmax); } diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java index 2c63ddb..78d34e2 100755 --- a/src/jalview/schemes/NucleotideColourScheme.java +++ b/src/jalview/schemes/NucleotideColourScheme.java @@ -34,7 +34,7 @@ public class NucleotideColourScheme extends ResidueColourScheme */ public NucleotideColourScheme() { - super(ResidueProperties.nucleotide, 0); + super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide, 0); } /** diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java index 0498536..7720220 100644 --- a/src/jalview/schemes/PurinePyrimidineColourScheme.java +++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java @@ -31,7 +31,7 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme */ public PurinePyrimidineColourScheme() { - super(ResidueProperties.purinepyrimidine, 0); + super(ResidueProperties.purinepyrimidineIndex, ResidueProperties.purinepyrimidine, 0); } /** diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index bbba865..666834e 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -35,7 +35,7 @@ import java.util.Map; */ public class ResidueColourScheme implements ColourSchemeI { - + final int[] symbolIndex; boolean conservationColouring = false; Color[] colors = null; @@ -58,23 +58,32 @@ public class ResidueColourScheme implements ColourSchemeI /** * Creates a new ResidueColourScheme object. - * + * @param final int[] index table into colors (ResidueProperties.naIndex or ResidueProperties.aaIndex) * @param colors - * DOCUMENT ME! + * colours for symbols in sequences * @param threshold - * DOCUMENT ME! + * threshold for conservation shading */ - public ResidueColourScheme(Color[] colours, int threshold) + public ResidueColourScheme(int[] aaOrnaIndex, Color[] colours, int threshold) { + symbolIndex = aaOrnaIndex; this.colors = colours; this.threshold = threshold; } /** - * Creates a new ResidueColourScheme object. + * Creates a new ResidueColourScheme object with a lookup table for indexing the colour map + */ + public ResidueColourScheme(int[] aaOrNaIndex) + { + symbolIndex = aaOrNaIndex; + } + /** + * Creates a new ResidueColourScheme object - default constructor for non-sequence dependent colourschemes */ public ResidueColourScheme() { + symbolIndex = null; } /** @@ -83,7 +92,7 @@ public class ResidueColourScheme implements ColourSchemeI public Color findColour(char c) { return colors == null ? Color.white - : colors[ResidueProperties.aaIndex[c]]; + : colors[symbolIndex[c]]; } @Override @@ -91,9 +100,9 @@ public class ResidueColourScheme implements ColourSchemeI { Color currentColour; - if ((threshold == 0) || aboveThreshold(c, j)) + if (colors!=null && symbolIndex!=null && (threshold == 0) || aboveThreshold(c, j)) { - currentColour = colors[ResidueProperties.aaIndex[c]]; + currentColour = colors[symbolIndex[c]]; } else { diff --git a/src/jalview/schemes/ScoreColourScheme.java b/src/jalview/schemes/ScoreColourScheme.java index 116bbd8..d11a2e8 100755 --- a/src/jalview/schemes/ScoreColourScheme.java +++ b/src/jalview/schemes/ScoreColourScheme.java @@ -48,9 +48,9 @@ public class ScoreColourScheme extends ResidueColourScheme * @param max * DOCUMENT ME! */ - public ScoreColourScheme(double[] scores, double min, double max) + public ScoreColourScheme(int symbolIndex[], double[] scores, double min, double max) { - super(); + super(symbolIndex); this.scores = scores; this.min = min; diff --git a/src/jalview/schemes/StrandColourScheme.java b/src/jalview/schemes/StrandColourScheme.java index ef88c38..69c2f1c 100755 --- a/src/jalview/schemes/StrandColourScheme.java +++ b/src/jalview/schemes/StrandColourScheme.java @@ -32,7 +32,7 @@ public class StrandColourScheme extends ScoreColourScheme */ public StrandColourScheme() { - super(ResidueProperties.strand, ResidueProperties.strandmin, + super(ResidueProperties.aaIndex, ResidueProperties.strand, ResidueProperties.strandmin, ResidueProperties.strandmax); } diff --git a/src/jalview/schemes/TaylorColourScheme.java b/src/jalview/schemes/TaylorColourScheme.java index ceee169..316c828 100755 --- a/src/jalview/schemes/TaylorColourScheme.java +++ b/src/jalview/schemes/TaylorColourScheme.java @@ -21,6 +21,6 @@ public class TaylorColourScheme extends ResidueColourScheme { public TaylorColourScheme() { - super(ResidueProperties.taylor, 0); + super(ResidueProperties.aaIndex, ResidueProperties.taylor, 0); } } diff --git a/src/jalview/schemes/TurnColourScheme.java b/src/jalview/schemes/TurnColourScheme.java index a2c1eda..cd5cd3f 100755 --- a/src/jalview/schemes/TurnColourScheme.java +++ b/src/jalview/schemes/TurnColourScheme.java @@ -32,7 +32,7 @@ public class TurnColourScheme extends ScoreColourScheme */ public TurnColourScheme() { - super(ResidueProperties.turn, ResidueProperties.turnmin, + super(ResidueProperties.aaIndex,ResidueProperties.turn, ResidueProperties.turnmin, ResidueProperties.turnmax); } diff --git a/src/jalview/schemes/ZappoColourScheme.java b/src/jalview/schemes/ZappoColourScheme.java index c6dffe5..c578fe3 100755 --- a/src/jalview/schemes/ZappoColourScheme.java +++ b/src/jalview/schemes/ZappoColourScheme.java @@ -30,6 +30,6 @@ public class ZappoColourScheme extends ResidueColourScheme */ public ZappoColourScheme() { - super(ResidueProperties.zappo, 0); + super(ResidueProperties.aaIndex, ResidueProperties.zappo, 0); } } -- 1.7.10.2