X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=90808def4fed87ef0f60554585ca59fb30096732;hb=fb0704b01deb0caee842b5b3eefb86e24af97c96;hp=a46aa921c837a3611425049b58e013fb3cd1364a;hpb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index a46aa92..90808de 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,4 +1,20 @@ - +/* + * 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.renderer; import jalview.analysis.AAFrequency; @@ -35,7 +51,6 @@ public class AnnotationRenderer int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { - g.setColor(STEM_COLOUR); int sCol = (lastSSX / charWidth) + startRes; int x1 = lastSSX; @@ -276,6 +291,7 @@ public class AnnotationRenderer /** * Render the annotation rows associated with an alignment. + * * @param annotPanel * container frame * @param av @@ -288,12 +304,14 @@ public class AnnotationRenderer * first column that will be drawn * @param endRes * last column that will be drawn - * @return true if the fadedImage was used for any alignment annotation rows currently being calculated + * @return true if the fadedImage was used for any alignment annotation rows + * currently being calculated */ - public boolean drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, - Graphics g, int activeRow, int startRes, int endRes) + public boolean drawComponent(AwtRenderPanelI annotPanel, + AlignViewportI av, Graphics g, int activeRow, int startRes, + int endRes) { - boolean usedFaded=false; + boolean usedFaded = false; // NOTES: // AnnotationPanel needs to implement: ImageObserver, access to // AlignViewport @@ -321,7 +339,7 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - Annotation[] row_annotations=row.annotations; + Annotation[] row_annotations = row.annotations; if (!row.visible) { continue; @@ -360,7 +378,7 @@ public class AnnotationRenderer if (row.autoCalculated && av.isCalculationInProgress(row)) { y += charHeight; - usedFaded=true; + usedFaded = true; g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - row.height, imgWidth, y, annotationPanel); g.setColor(Color.black); @@ -372,22 +390,22 @@ public class AnnotationRenderer /* * else if (annotationPanel.av.updatingConservation && * aa[i].label.equals("Conservation")) { - * + * * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y - * row.height, annotationPanel.imgWidth, y, 0, y - row.height, * annotationPanel.imgWidth, y, annotationPanel); - * + * * g.setColor(Color.black); // * g.drawString("Calculating Conservation.....",20, y-row.height/2); - * + * * continue; } else if (annotationPanel.av.updatingConservation && * aa[i].label.equals("Quality")) { - * + * * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y - * row.height, annotationPanel.imgWidth, y, 0, y - row.height, * annotationPanel.imgWidth, y, annotationPanel); g.setColor(Color.black); * // / g.drawString("Calculating Quality....",20, y-row.height/2); - * + * * continue; } */ // first pass sets up state for drawing continuation from left-hand column @@ -789,19 +807,23 @@ public class AnnotationRenderer switch (lastSS) { case 'H': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawHelixAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, validEnd); break; case 'E': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawSheetAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, validEnd); break; case '(': // Stem case for RNA secondary structure case ')': // and opposite direction drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); +// case 'S': // Stem case for RNA secondary structure +// case 's': // and opposite direction +// drawStemAnnot(g, row_annotations, lastSSX, x, y, +// iconOffset, startRes, column, validRes, validEnd); break; case '{': case '}': @@ -917,18 +939,18 @@ public class AnnotationRenderer switch (lastSS) { case 'H': - drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); break; case 'E': - drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); break; case 's': case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); break; case '{': case '}': @@ -992,8 +1014,8 @@ public class AnnotationRenderer column, validRes, validEnd); break; default: - drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); + drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); break; } } @@ -1030,8 +1052,8 @@ public class AnnotationRenderer { if (aa[gg].graphGroup == row.graphGroup) { - drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, - groupmax, row.graphHeight); + drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, + endRes, y, groupmin, groupmax, row.graphHeight); } } @@ -1039,14 +1061,14 @@ public class AnnotationRenderer } else { - drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin, - row.graphMax, row.graphHeight); + drawLineGraph(g, row, row_annotations, startRes, endRes, y, + row.graphMin, row.graphMax, row.graphHeight); } } else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { - drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin, - row.graphMax, y); + drawBarGraph(g, row, row_annotations, startRes, endRes, + row.graphMin, row.graphMax, y); } } @@ -1073,22 +1095,21 @@ public class AnnotationRenderer private Color sdNOTCANONICAL_COLOUR; - public void drawGlyphLine(Graphics g, Annotation[] row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, + int x, int y, int iconOffset, int startRes, int column, + boolean validRes, boolean validEnd) { g.setColor(GLYPHLINE_COLOR); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); } - public void drawSheetAnnot(Graphics g, Annotation[] row, - - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX, + int x, int y, int iconOffset, int startRes, int column, + boolean validRes, boolean validEnd) { g.setColor(SHEET_COLOUR); - if (!validEnd || !validRes || row==null || row[column] == null + if (!validEnd || !validRes || row == null || row[column] == null || row[column].secondaryStructure != 'E') { g.fillRect(lastSSX, y + 4 + iconOffset, @@ -1107,9 +1128,9 @@ public class AnnotationRenderer } - public void drawHelixAnnot(Graphics g, Annotation[] row, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) + public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, + int x, int y, int iconOffset, int startRes, int column, + boolean validRes, boolean validEnd) { g.setColor(HELIX_COLOUR); @@ -1167,8 +1188,9 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } - public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, - int eRes, int y, float min, float max, int graphHeight) + public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, + Annotation[] aa_annotations, int sRes, int eRes, int y, + float min, float max, int graphHeight) { if (sRes > aa_annotations.length) { @@ -1256,8 +1278,9 @@ public class AnnotationRenderer } } - public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, - int eRes, float min, float max, int y) + public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, + Annotation[] aa_annotations, int sRes, int eRes, float min, + float max, int y) { if (sRes > aa_annotations.length) { @@ -1393,7 +1416,7 @@ public class AnnotationRenderer // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, // (int)(scl)); // g.setColor(profcolour.findColour(dc[0]).darker()); - g.setColor(profcolour.findColour(dc[0], column,null)); + g.setColor(profcolour.findColour(dc[0], column, null)); hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm .getBaselineIndex()])); @@ -1414,15 +1437,16 @@ public class AnnotationRenderer BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); - y2 = (int) (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight); + y2 = (int) (y - ((_aa.threshold.value - min) / range) + * _aa.graphHeight); g.drawLine(0, y2, (eRes - sRes) * charWidth, y2); g2.setStroke(new BasicStroke()); } } // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int width, - int y, int sRes, int eRes) + public void drawGraph(Graphics g, AlignmentAnnotation _aa, + Annotation[] aa_annotations, int width, int y, int sRes, int eRes) { eRes = Math.min(eRes, aa_annotations.length); g.setColor(Color.white);