X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=9c5512c350c5bd862253d4dd26eef8c182354204;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=06085da1641c691534021126ef430f883ec743af;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 06085da..9c5512c 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,203 +1,318 @@
-/*
- * 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.datamodel.*;
-
-public class AnnotationColourGradient
- extends ResidueColourScheme
-{
- public static int NO_THRESHOLD = -1;
- public static int BELOW_THRESHOLD = 0;
- public static int ABOVE_THRESHOLD = 1;
-
- AlignmentAnnotation annotation;
- int aboveAnnotationThreshold = -1;
-
- GraphLine annotationThreshold;
-
- float r1, g1, b1, rr, gg, bb, dr, dg, db;
- float range = 0;
-
- ColourSchemeI colourScheme;
-
- /**
- * Creates a new AnnotationColourGradient object.
- */
- public AnnotationColourGradient(AlignmentAnnotation annotation,
- ColourSchemeI originalColour,
- int aboveThreshold)
- {
- if (originalColour instanceof AnnotationColourGradient)
- {
- colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;
- }
- else
- {
- colourScheme = originalColour;
- }
-
- this.annotation = annotation;
-
- aboveAnnotationThreshold = aboveThreshold;
-
- if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
- {
- annotationThreshold = annotation.threshold;
- }
- }
-
- /**
- * Creates a new AnnotationColourGradient object.
- */
- public AnnotationColourGradient(AlignmentAnnotation annotation,
- Color minColour, Color maxColour,
- int aboveThreshold)
- {
- this.annotation = annotation;
-
- aboveAnnotationThreshold = aboveThreshold;
-
- if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
- {
- annotationThreshold = annotation.threshold;
- }
-
- r1 = minColour.getRed();
- g1 = minColour.getGreen();
- b1 = minColour.getBlue();
-
- rr = maxColour.getRed() - r1;
- gg = maxColour.getGreen() - g1;
- bb = maxColour.getBlue() - b1;
-
- range = annotation.graphMax - annotation.graphMin;
-
- }
-
- public String getAnnotation()
- {
- return annotation.label;
- }
-
- public int getAboveThreshold()
- {
- return aboveAnnotationThreshold;
- }
-
- public float getAnnotationThreshold()
- {
- if (annotationThreshold == null)
- {
- return 0;
- }
- else
- {
- return annotationThreshold.value;
- }
- }
-
- public ColourSchemeI getBaseColour()
- {
- return colourScheme;
- }
-
- public Color getMinColour()
- {
- return new Color( (int) r1, (int) g1, (int) b1);
- }
-
- public Color getMaxColour()
- {
- return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(char c)
- {
- return Color.red;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n DOCUMENT ME!
- * @param j DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Color findColour(char c, int j)
- {
- Color currentColour = Color.white;
-
- if ( (threshold == 0) || aboveThreshold(c, j))
- {
- if (j < annotation.annotations.length
- && annotation.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
- {
- if (aboveAnnotationThreshold == NO_THRESHOLD
- ||
- (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&
- annotation.annotations[j].value >= annotationThreshold.value)
- ||
- (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&
- annotation.annotations[j].value <= annotationThreshold.value))
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j);
- }
- else if (range != 0)
- {
- dr = rr *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + r1;
- dg = gg *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + g1;
- db = bb *
- ( (annotation.annotations[j].value - annotation.graphMin) /
- range)
- + b1;
-
- currentColour = new Color( (int) dr, (int) dg, (int) db);
- }
- }
- }
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package jalview.schemes;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Map;
+
+public class AnnotationColourGradient extends ResidueColourScheme
+{
+ public static final int NO_THRESHOLD = -1;
+
+ public static final int BELOW_THRESHOLD = 0;
+
+ public static final int ABOVE_THRESHOLD = 1;
+
+ public AlignmentAnnotation annotation;
+
+ int aboveAnnotationThreshold = -1;
+
+ public boolean thresholdIsMinMax = false;
+
+ GraphLine annotationThreshold;
+
+ float r1, g1, b1, rr, gg, bb, dr, dg, db;
+
+ ColourSchemeI colourScheme;
+
+ private boolean predefinedColours = false;
+
+ private boolean seqAssociated = false;
+
+ IdentityHashMap seqannot = null;
+
+ /**
+ * Creates a new AnnotationColourGradient object.
+ */
+ public AnnotationColourGradient(AlignmentAnnotation annotation,
+ ColourSchemeI originalColour, int aboveThreshold)
+ {
+ if (originalColour instanceof AnnotationColourGradient)
+ {
+ colourScheme = ((AnnotationColourGradient) originalColour).colourScheme;
+ }
+ else
+ {
+ colourScheme = originalColour;
+ }
+
+ this.annotation = annotation;
+
+ aboveAnnotationThreshold = aboveThreshold;
+
+ if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+ {
+ annotationThreshold = annotation.threshold;
+ }
+ }
+
+ /**
+ * Creates a new AnnotationColourGradient object.
+ */
+ public AnnotationColourGradient(AlignmentAnnotation annotation,
+ Color minColour, Color maxColour, int aboveThreshold)
+ {
+ this.annotation = annotation;
+
+ aboveAnnotationThreshold = aboveThreshold;
+
+ if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)
+ {
+ annotationThreshold = annotation.threshold;
+ }
+
+ r1 = minColour.getRed();
+ g1 = minColour.getGreen();
+ b1 = minColour.getBlue();
+
+ rr = maxColour.getRed() - r1;
+ gg = maxColour.getGreen() - g1;
+ bb = maxColour.getBlue() - b1;
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map hiddenReps)
+ {
+ // TODO Auto-generated method stub
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ else
+ {
+ seqannot = new IdentityHashMap();
+ }
+ for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+ .getCalcId()))
+ {
+ if (alan.sequenceRef != null
+ && (alan.label != null && annotation != null && alan.label
+ .equals(annotation.label)))
+ {
+ seqannot.put(alan.sequenceRef, alan);
+ }
+ }
+ }
+ }
+
+ public String getAnnotation()
+ {
+ return annotation.label;
+ }
+
+ public int getAboveThreshold()
+ {
+ return aboveAnnotationThreshold;
+ }
+
+ public float getAnnotationThreshold()
+ {
+ if (annotationThreshold == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return annotationThreshold.value;
+ }
+ }
+
+ public ColourSchemeI getBaseColour()
+ {
+ return colourScheme;
+ }
+
+ public Color getMinColour()
+ {
+ return new Color((int) r1, (int) g1, (int) b1);
+ }
+
+ public Color getMaxColour()
+ {
+ return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Color findColour(char c)
+ {
+ return Color.red;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param n
+ * DOCUMENT ME!
+ * @param j
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Color findColour(char c, int j, SequenceI seq)
+ {
+ Color currentColour = Color.white;
+ AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+ : this.annotation);
+ if (annotation == null)
+ {
+ return currentColour;
+ }
+ if ((threshold == 0) || aboveThreshold(c, j))
+ {
+ if (j < annotation.annotations.length
+ && annotation.annotations[j] != null
+ && !jalview.util.Comparison.isGap(c))
+ {
+
+ if (predefinedColours)
+ {
+ if (annotation.annotations[j].colour != null)
+ return annotation.annotations[j].colour;
+ else
+ return currentColour;
+ }
+
+ if (aboveAnnotationThreshold == NO_THRESHOLD
+ || (annotationThreshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
+ || (annotationThreshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+ {
+
+ float range = 1f;
+ if (thresholdIsMinMax
+ && annotation.threshold != null
+ && aboveAnnotationThreshold == ABOVE_THRESHOLD
+ && annotation.annotations[j].value >= annotation.threshold.value)
+ {
+ range = (annotation.annotations[j].value - annotation.threshold.value)
+ / (annotation.graphMax - annotation.threshold.value);
+ }
+ else if (thresholdIsMinMax && annotation.threshold != null
+ && aboveAnnotationThreshold == BELOW_THRESHOLD
+ && annotation.annotations[j].value >= annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.threshold.value - annotation.graphMin);
+ }
+ else
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+
+ if (colourScheme != null)
+ {
+ currentColour = colourScheme.findColour(c, j, seq);
+ }
+ else
+ {
+ dr = rr * range + r1;
+ dg = gg * range + g1;
+ db = bb * range + b1;
+
+ currentColour = new Color((int) dr, (int) dg, (int) db);
+ }
+ }
+ }
+ }
+
+ if (conservationColouring)
+ {
+ currentColour = applyConservation(currentColour, j);
+ }
+
+ return currentColour;
+ }
+
+ public boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ public void setPredefinedColours(boolean predefinedColours)
+ {
+ this.predefinedColours = predefinedColours;
+ }
+
+ public boolean isSeqAssociated()
+ {
+ return seqAssociated;
+ }
+
+ public void setSeqAssociated(boolean sassoc)
+ {
+ seqAssociated = sassoc;
+ }
+ @Override
+ public void setConsensus(Hashtable[] consensus)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConsensus(consensus);
+ }
+ }
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservation(cons);
+ }
+ }
+ @Override
+ public void setConservationInc(int i)
+ {
+ if (colourScheme!=null)
+ {
+ colourScheme.setConservationInc(i);
+ }
+ }
+}