-/*\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
- AlignmentAnnotation annotation;\r
- int aboveAnnotationThreshold = -1;\r
-\r
- GraphLine annotationThreshold;\r
-\r
- float r1, g1, b1, rr, gg, bb, dr, dg, db;\r
- float range = 0;\r
-\r
- ColourSchemeI colourScheme;\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
- range = annotation.graphMax - annotation.graphMin;\r
-\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
- 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
- if (colourScheme != null)\r
- {\r
- currentColour = colourScheme.findColour(c, j);\r
- }\r
- else if (range != 0)\r
- {\r
- dr = rr *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + r1;\r
- dg = gg *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + g1;\r
- db = bb *\r
- ( (annotation.annotations[j].value - annotation.graphMin) /\r
- range)\r
- + 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 ($$Version-Rel$$)
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.IdentityHashMap;
+import java.util.Map;
+
+public class AnnotationColourGradient extends FollowerColourScheme
+{
+ 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;
+
+ private boolean predefinedColours = false;
+
+ private boolean seqAssociated = false;
+ /**
+ * false if the scheme was constructed without a minColour and maxColour used
+ * to decide if existing colours should be taken from annotation elements when
+ * they exist
+ */
+ private boolean noGradient = false;
+ IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+ colourScheme, aboveAnnotationThreshold);
+ acg.thresholdIsMinMax = thresholdIsMinMax;
+ acg.annotationThreshold = (annotationThreshold == null) ? null
+ : new GraphLine(annotationThreshold);
+ acg.r1 = r1;
+ acg.g1 = g1;
+ acg.b1 = b1;
+ acg.rr = rr;
+ acg.gg = gg;
+ acg.bb = bb;
+ acg.predefinedColours = predefinedColours;
+ acg.seqAssociated = seqAssociated;
+ acg.noGradient = noGradient;
+ return acg;
+ }
+
+ /**
+ * 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;
+ }
+ // clear values so we don't get weird black bands...
+ r1 = 254;
+ g1 = 254;
+ b1 = 254;
+ rr = 0;
+ gg = 0;
+ bb = 0;
+
+ noGradient = true;
+ }
+
+ /**
+ * 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;
+
+ noGradient = false;
+ aamax = annotation.graphMax;
+ aamin = annotation.graphMin;
+ if (annotation.isRNA())
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
+ }
+
+ @Override
+ public void alignmentChanged(AnnotatedCollectionI alignment,
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ super.alignmentChanged(alignment, hiddenReps);
+
+ if (seqAssociated && annotation.getCalcId() != null)
+ {
+ if (seqannot != null)
+ {
+ seqannot.clear();
+ }
+ else
+ {
+ seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+ }
+ // resolve the context containing all the annotation for the sequence
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ boolean f = true,rna=false;
+ for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
+ .getCalcId()))
+ {
+ if (alan.sequenceRef != null
+ && (alan.label != null && annotation != null && alan.label
+ .equals(annotation.label)))
+ {
+ if (!rna && alan.isRNA())
+ {
+ rna = true;
+ }
+ seqannot.put(alan.sequenceRef, alan);
+ if (f || alan.graphMax > aamax)
+ {
+ aamax = alan.graphMax;
+ }
+ if (f || alan.graphMin < aamin)
+ {
+ aamin = alan.graphMin;
+ }
+ f = false;
+ }
+ }
+ if (rna)
+ {
+ ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+ }
+ }
+ }
+
+ float aamin = 0f, aamax = 0f;
+ public String getAnnotation()
+ {
+ return annotation.label;
+ }
+
+ public int getAboveThreshold()
+ {
+ return aboveAnnotationThreshold;
+ }
+
+ public float getAnnotationThreshold()
+ {
+ if (annotationThreshold == null)
+ {
+ return 0;
+ }
+ else
+ {
+ return annotationThreshold.value;
+ }
+ }
+
+ 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 != null ? seqannot
+ .get(seq) : this.annotation);
+ if (annotation == null) {
+ return currentColour;
+ }
+ if ((threshold == 0) || aboveThreshold(c, j)) {
+ if (annotation.annotations != null && j < annotation.annotations.length
+ && annotation.annotations[j] != null && !Comparison.isGap(c)) {
+ Annotation aj = annotation.annotations[j];
+ // 'use original colours' => colourScheme != null
+ // -> look up colour to be used
+ // predefined colours => preconfigured shading
+ // -> only use original colours reference if thresholding enabled &
+ // minmax exists
+ // annotation.hasIcons => null or black colours replaced with glyph
+ // colours
+ // -> reuse original colours if present
+ // -> if thresholding enabled then return colour on non-whitespace glyph
+
+ if (aboveAnnotationThreshold == NO_THRESHOLD
+ || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+ : aj.value <= annotationThreshold.value))) {
+ if (predefinedColours && aj.colour != null
+ && !aj.colour.equals(Color.black)) {
+ currentColour = aj.colour;
+ } else if (annotation.hasIcons
+ && annotation.graph == AlignmentAnnotation.NO_GRAPH) {
+ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+ && aj.secondaryStructure != '-') {
+ if (colourScheme != null) {
+ currentColour = colourScheme.findColour(c, j, seq);
+ } else {
+ if (annotation.isRNA()) {
+ currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
+ } else {
+ currentColour = annotation.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
+ : annotation.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+ : AnnotationRenderer.STEM_COLOUR;
+ }
+ }
+ } else {
+ //
+ return Color.white;
+ }
+ } else if (noGradient) {
+ if (colourScheme != null) {
+ currentColour = colourScheme.findColour(c, j, seq);
+ } else {
+ if (aj.colour != null) {
+ currentColour = aj.colour;
+ }
+ }
+ } else {
+ currentColour = shadeCalculation(annotation, j);
+ }
+ }
+ if (conservationColouring) {
+ currentColour = applyConservation(currentColour, j);
+ }
+ }
+ }
+ return currentColour;
+ }
+
+ private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ {
+
+ // calculate a shade
+ 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
+ {
+ if (annotation.graphMax != annotation.graphMin)
+ {
+ range = (annotation.annotations[j].value - annotation.graphMin)
+ / (annotation.graphMax - annotation.graphMin);
+ }
+ else
+ {
+ range = 0f;
+ }
+ }
+
+ int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+ * range + b1);
+
+ return new Color(dr, dg, db);
+
+ }
+ 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff