X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPIDColourScheme.java;h=657d6b0dc49a6771cd1f6f0a4449d3a4a240f022;hb=a42904684c75b2729d763af933e5a991a3424f67;hp=e1dbf4696706b9cd4b8c96bb4a6cf7f76d8a04cf;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index e1dbf46..657d6b0 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -1,94 +1,107 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-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 findColour(char c, int j)
- {
- if ('a' <= c && c <= 'z')
- {
- c -= ('a' - 'A');
- }
-
- if (consensus == null
- || j >= consensus.length
- || consensus[j] == null)
- {
- return Color.white;
- }
-
- if ( (threshold != 0) && !aboveThreshold(c, j))
- {
- return Color.white;
- }
-
- Color currentColour = Color.white;
-
- double sc = 0;
-
- if (consensus.length <= j)
- {
- return Color.white;
- }
-
- if ( (Integer.parseInt(consensus[j].get(AAFrequency.MAXCOUNT).toString()) !=
- -1) &&
- consensus[j].contains(String.valueOf(c)))
- {
- sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
-
- if (!jalview.util.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;
- }
-}
+/*
+ * 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.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
+{
+ private static final Color[] pidColours = { new Color(100, 100, 255),
+ new Color(153, 153, 255), new Color(204, 204, 255), };
+
+ private static final float[] thresholds = { 80, 60, 40, };
+
+ SequenceGroup group;
+
+ public PIDColourScheme()
+ {
+ }
+
+ @Override
+ public Color findColour(char c, int j, SequenceI seq,
+ String consensusResidue, float pid)
+ {
+ /*
+ * compare as upper case; note consensusResidue is
+ * always computed as uppercase
+ */
+ if ('a' <= c && c <= 'z')
+ {
+ c -= ('a' - 'A');
+ }
+
+ if (consensusResidue == null || Comparison.isGap(c))
+ {
+ return Color.white;
+ }
+
+ Color colour = Color.white;
+
+ /*
+ * test whether this is the consensus (or joint consensus) residue
+ */
+ boolean matchesConsensus = consensusResidue.contains(
+ String.valueOf(c));
+ if (matchesConsensus)
+ {
+ for (int i = 0; i < thresholds.length; i++)
+ {
+ if (pid > thresholds[i])
+ {
+ colour = pidColours[i];
+ break;
+ }
+ }
+ }
+
+ return colour;
+ }
+
+ @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;
+ }
+}