X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=389655c53314b18c7da9b7ff28f096b1fa727f35;hb=89911f9bb8cd7c981cbeefb0445af265fc2b0d0b;hp=312ae7d534ce8a8ce8bcc38419e4063788c9f262;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 312ae7d..389655c 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,61 +1,123 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-
-import java.util.*;
-import java.awt.*;
-
-public class PIDColourScheme extends ResidueColourScheme {
- public Color[] pidColours;
- public float[] thresholds;
-
- SequenceGroup group;
-
- public PIDColourScheme() {
- this.pidColours = ResidueProperties.pidColours;
- this.thresholds = ResidueProperties.pidThresholds;
- }
- public Color getColour(SequenceI seq, int j,Vector aa) {
- Color c = Color.white;
-
- String s = seq.getSequence(j,j+1);
-
- if (aa != null && j < aa.size()) {
- c = findColour(seq,s,j,aa);
- }
-
- return c;
- }
-
- public Color findColour(SequenceI seq,String s, int j,Vector aa) {
- Color c = Color.white;
- Hashtable hash = null;
-
- if (aa != null) {
- hash = (Hashtable)aa.elementAt(j);
- }
- else
- return c;
-
- String max = (String)hash.get("maxResidue");
-
- double sc = 0;
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {
- sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));
-
- // MC Should be isGap
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {
- for (int i=0; i < thresholds.length; i++) {
- if (sc > thresholds[i]) {
- c = pidColours[i];
- break;
- }
- }
- } else {
- c = Color.white;
- }
- }
- return c;
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfileI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+public class PIDColourScheme extends ResidueColourScheme
+{
+ public Color[] pidColours;
+
+ public float[] thresholds;
+
+ SequenceGroup group;
+
+ public PIDColourScheme()
+ {
+ this.pidColours = ResidueProperties.pidColours;
+ this.thresholds = ResidueProperties.pidThresholds;
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= ('a' - 'A');
+ }
+
+ if (consensus == null || consensus.get(j) == null)
+ {
+ return Color.white;
+ }
+
+ if ((threshold != 0) && !aboveThreshold(c, j))
+ {
+ return Color.white;
+ }
+
+ Color currentColour = Color.white;
+
+ double sc = 0;
+
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ ProfileI profile = consensus.get(j);
+ boolean matchesConsensus = profile.getModalResidue().contains(
+ String.valueOf(c));
+ if (matchesConsensus)
+ {
+ sc = profile.getPercentageIdentity(ignoreGaps);
+
+ if (!Comparison.isGap(c))
+ {
+ for (int i = 0; i < thresholds.length; i++)
+ {
+ if (sc > thresholds[i])
+ {
+ currentColour = pidColours[i];
+ break;
+ }
+ }
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.PID.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map hrs)
+ {
+ return new PIDColourScheme();
+ }
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
+}