-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemes;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationColourGradient\r
- extends ResidueColourScheme\r
-{\r
- public static int NO_THRESHOLD = -1;\r
- public static int BELOW_THRESHOLD = 0;\r
- public static int ABOVE_THRESHOLD = 1;\r
-\r
- public AlignmentAnnotation annotation;\r
- int aboveAnnotationThreshold = -1;\r
- public boolean thresholdIsMinMax = false;\r
-\r
- GraphLine annotationThreshold;\r
-\r
- float r1, g1, b1, rr, gg, bb, dr, dg, db;\r
-\r
- ColourSchemeI colourScheme;\r
-\r
- public boolean predefinedColours = false;\r
-\r
- /**\r
- * Creates a new AnnotationColourGradient object.\r
- */\r
- public AnnotationColourGradient(AlignmentAnnotation annotation,\r
- ColourSchemeI originalColour,\r
- int aboveThreshold)\r
- {\r
- if (originalColour instanceof AnnotationColourGradient)\r
- {\r
- colourScheme = ( (AnnotationColourGradient) originalColour).colourScheme;\r
- }\r
- else\r
- {\r
- colourScheme = originalColour;\r
- }\r
-\r
- this.annotation = annotation;\r
-\r
- aboveAnnotationThreshold = aboveThreshold;\r
-\r
- if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)\r
- {\r
- annotationThreshold = annotation.threshold;\r
- }\r
- }\r
-\r
- /**\r
- * Creates a new AnnotationColourGradient object.\r
- */\r
- public AnnotationColourGradient(AlignmentAnnotation annotation,\r
- Color minColour, Color maxColour,\r
- int aboveThreshold)\r
- {\r
- this.annotation = annotation;\r
-\r
- aboveAnnotationThreshold = aboveThreshold;\r
-\r
- if (aboveThreshold != NO_THRESHOLD && annotation.threshold != null)\r
- {\r
- annotationThreshold = annotation.threshold;\r
- }\r
-\r
- r1 = minColour.getRed();\r
- g1 = minColour.getGreen();\r
- b1 = minColour.getBlue();\r
-\r
- rr = maxColour.getRed() - r1;\r
- gg = maxColour.getGreen() - g1;\r
- bb = maxColour.getBlue() - b1;\r
- }\r
-\r
- public String getAnnotation()\r
- {\r
- return annotation.label;\r
- }\r
-\r
- public int getAboveThreshold()\r
- {\r
- return aboveAnnotationThreshold;\r
- }\r
-\r
- public float getAnnotationThreshold()\r
- {\r
- if (annotationThreshold == null)\r
- {\r
- return 0;\r
- }\r
- else\r
- {\r
- return annotationThreshold.value;\r
- }\r
- }\r
-\r
- public ColourSchemeI getBaseColour()\r
- {\r
- return colourScheme;\r
- }\r
-\r
- public Color getMinColour()\r
- {\r
- return new Color( (int) r1, (int) g1, (int) b1);\r
- }\r
-\r
- public Color getMaxColour()\r
- {\r
- return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(char c)\r
- {\r
- return Color.red;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- * @param j DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color findColour(char c, int j)\r
- {\r
- Color currentColour = Color.white;\r
-\r
- if ( (threshold == 0) || aboveThreshold(c, j))\r
- {\r
- if (j < annotation.annotations.length\r
- && annotation.annotations[j] != null\r
- && !jalview.util.Comparison.isGap(c))\r
- {\r
-\r
- if (predefinedColours)\r
- {\r
- if(annotation.annotations[j].colour != null)\r
- return annotation.annotations[j].colour;\r
- else\r
- return currentColour;\r
- }\r
-\r
- if (aboveAnnotationThreshold == NO_THRESHOLD\r
- ||\r
- (annotationThreshold != null && aboveAnnotationThreshold == ABOVE_THRESHOLD &&\r
- annotation.annotations[j].value >= annotationThreshold.value)\r
- ||\r
- (annotationThreshold != null && aboveAnnotationThreshold == BELOW_THRESHOLD &&\r
- annotation.annotations[j].value <= annotationThreshold.value))\r
- {\r
-\r
- float range=1f;\r
- if (thresholdIsMinMax\r
- && annotation.threshold != null\r
- && aboveAnnotationThreshold == ABOVE_THRESHOLD\r
- && annotation.annotations[j].value>annotation.threshold.value)\r
- {\r
- range =\r
- (annotation.annotations[j].value - annotation.threshold.value) /\r
- (annotation.graphMax - annotation.threshold.value);\r
- }\r
- else if (thresholdIsMinMax\r
- && annotation.threshold != null\r
- && aboveAnnotationThreshold == BELOW_THRESHOLD\r
- && annotation.annotations[j].value > annotation.graphMin)\r
- {\r
- range =\r
- ( annotation.annotations[j].value - annotation.graphMin ) /\r
- (annotation.threshold.value - annotation.graphMin );\r
- }\r
- else\r
- {\r
- range = (annotation.annotations[j].value -\r
- annotation.graphMin) /\r
- (annotation.graphMax - annotation.graphMin);\r
- }\r
-\r
-\r
- if (colourScheme != null)\r
- {\r
- currentColour = colourScheme.findColour(c, j);\r
- }\r
- else if (range != 0)\r
- {\r
- dr = rr * range + r1;\r
- dg = gg * range + g1;\r
- db = bb * range + b1;\r
-\r
- currentColour = new Color( (int) dr, (int) dg, (int) db);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (conservationColouring)\r
- {\r
- currentColour = applyConservation(currentColour, j);\r
- }\r
-\r
- return currentColour;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+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.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;
+
+ public boolean predefinedColours = false;
+
+ public boolean seqAssociated = false;
+
+ IdentityHashMap<SequenceI, AlignmentAnnotation> 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<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ // TODO Auto-generated method stub
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ else
+ {
+ seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ }
+ 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 isSeqAssociated()
+ {
+ return seqAssociated;
+ }
+
+ public void setSeqAssociated(boolean sassoc)
+ {
+ seqAssociated = sassoc;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff