From: jprocter Date: Fri, 28 Oct 2011 14:43:40 +0000 (+0100) Subject: (JAL-889) ensure latest version of RNA pairlist is used to generate helical colouring X-Git-Tag: Jalview_2_9~565^2~10 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7ddb4e421ed93f92b6a94f13f11c6f5677e2a0b;p=jalview.git (JAL-889) ensure latest version of RNA pairlist is used to generate helical colouring --- diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java index 774fc95..16f822f 100644 --- a/src/jalview/schemes/RNAHelicesColour.java +++ b/src/jalview/schemes/RNAHelicesColour.java @@ -57,39 +57,56 @@ public class RNAHelicesColour extends ResidueColourScheme public RNAHelicesColour(AlignmentAnnotation annotation) { this.annotation = annotation; + refresh(); + } + + private long lastrefresh = -1; - // Figure out number of helices - // Length of rnasecstr is the number of pairs of positions that base pair - // with each other in the secondary structure - for (int x = 0; x < this.annotation._rnasecstr.length; x++) + public void refresh() + { + if (lastrefresh != annotation._rnasecstr.hashCode() && annotation.isValidStruc()) { + annotation.getRNAStruc(); + lastrefresh = annotation._rnasecstr.hashCode(); + numHelix = 0; + positionsToHelix = new Hashtable(); + + // Figure out number of helices + // Length of rnasecstr is the number of pairs of positions that base pair + // with each other in the secondary structure + for (int x = 0; x < this.annotation._rnasecstr.length; x++) + { - /* - * System.out.println(this.annotation._rnasecstr[x] + " Begin" + - * this.annotation._rnasecstr[x].getBegin()); - */ - // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); + /* + * System.out.println(this.annotation._rnasecstr[x] + " Begin" + + * this.annotation._rnasecstr[x].getBegin()); + */ + // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup()); - positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(), - this.annotation._rnasecstr[x].getFeatureGroup()); - positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(), - this.annotation._rnasecstr[x].getFeatureGroup()); + positionsToHelix.put(this.annotation._rnasecstr[x].getBegin(), + this.annotation._rnasecstr[x].getFeatureGroup()); + positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(), + this.annotation._rnasecstr[x].getFeatureGroup()); - if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix) - { - numHelix = Integer.parseInt(this.annotation._rnasecstr[x] - .getFeatureGroup()); - } + if (Integer.parseInt(this.annotation._rnasecstr[x] + .getFeatureGroup()) > numHelix) + { + numHelix = Integer.parseInt(this.annotation._rnasecstr[x] + .getFeatureGroup()); + } - } + } - // Generate random colors and store - for (int j = 0; j <= numHelix; j++) - { - helixcolorhash.put(Integer.toString(j), jalview.util.ColorUtils - .generateRandomColor(Color.white)); + // Generate random colors and store + for (int j = 0; j <= numHelix; j++) + { + if (!helixcolorhash.containsKey(Integer.toString(j))) + { + helixcolorhash.put(Integer.toString(j), + jalview.util.ColorUtils.generateRandomColor(Color.white)); + } + } } - } /** @@ -120,6 +137,7 @@ public class RNAHelicesColour extends ResidueColourScheme */ public Color findColour(char c, int j) { + refresh(); Color currentColour = Color.white; String currentHelix = null; currentHelix = (String) positionsToHelix.get(j);