X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=050e9f26dc861a1fec392e6577f535a3a397ef96;hpb=fa7f47950cccf7241aad97c1f6c99700e5a476f7;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 050e9f2..a88aa4a 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -29,6 +29,7 @@ import javax.swing.*; import com.stevesoft.pat.Regex; import jalview.analysis.AAFrequency; +import jalview.analysis.StructureFrequency; import jalview.datamodel.*; import jalview.schemes.ColourSchemeI; @@ -93,9 +94,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean mouseDragging = false; boolean MAC = false; - - //for editing cursor + + // for editing cursor int cursorX = 0; + int cursorY = 0; /** @@ -145,7 +147,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public int adjustPanelHeight() { - int height=calcPanelHeight(); + int height = calcPanelHeight(); this.setPreferredSize(new Dimension(1, height)); if (ap != null) { @@ -157,8 +159,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, } /** - * calculate the height for visible annotation, revalidating bounds where necessary - * ABSTRACT GUI METHOD + * calculate the height for visible annotation, revalidating bounds where + * necessary ABSTRACT GUI METHOD + * * @return total height of annotation */ public int calcPanelHeight() @@ -462,17 +465,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, /* * Just display the needed structure options */ - if(av.alignment.isNucleotide()==true){ - item = new JMenuItem(STEM); - item.addActionListener(this); - pop.add(item); - }else{ - item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); + if (av.alignment.isNucleotide() == true) + { + item = new JMenuItem(STEM); + item.addActionListener(this); + pop.add(item); + } + else + { + item = new JMenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(SHEET); + item.addActionListener(this); + pop.add(item); } item = new JMenuItem(LABEL); item.addActionListener(this); @@ -666,35 +672,39 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - if(activeRow !=-1){ - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - AlignmentAnnotation anot = aa[activeRow]; - - if(anot.description.equals("secondary structure")){ - //System.out.println(anot.description+" "+anot.getRNAStruc()); - } - } + if (activeRow != -1) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation anot = aa[activeRow]; + + if (anot.description.equals("secondary structure")) + { + // System.out.println(anot.description+" "+anot.getRNAStruc()); + } + } } - //TODO mouseClicked-content and drawCursor are quite experimental! - public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1) - { - int pady = av.charHeight / 5; - int charOffset = 0; - graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); - if (av.validCharWidth) - { - graphics.setColor(Color.white); + // TODO mouseClicked-content and drawCursor are quite experimental! + public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, + int y1) + { + int pady = av.charHeight / 5; + int charOffset = 0; + graphics.setColor(Color.black); + graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + + if (av.validCharWidth) + { + graphics.setColor(Color.white); - char s = seq.getCharAt(res); + char s = seq.getCharAt(res); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); - } + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + x1, + (y1 + av.charHeight) - pady); + } - } + } /** * DOCUMENT ME! @@ -870,7 +880,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean[] graphGroupDrawn = new boolean[aa.length]; int charOffset = 0; // offset for a label float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. + // column. Font ofont = g.getFont(); // \u03B2 \u03B1 for (int i = 0; i < aa.length; i++) @@ -1057,8 +1067,17 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (row.hasIcons) { - if (!validRes - || (row.annotations[column].secondaryStructure != lastSS)) + char ss = validRes ? row.annotations[column].secondaryStructure + : ' '; + if (ss == 'S') + { + // distinguish between forward/backward base-pairing + if (row.annotations[column].displayCharacter.indexOf(')') > -1) + { + ss = 's'; + } + } + if (!validRes || (ss != lastSS)) { if (x > -1) { @@ -1075,6 +1094,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, break; case 'S': // Stem case for RNA secondary structure + case 's': // and opposite direction drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; @@ -1089,7 +1109,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (validRes) { - lastSS = row.annotations[column].secondaryStructure; + lastSS = ss; } else { @@ -1101,11 +1121,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } } - column++; x++; } - if (column >= row.annotations.length) { column = row.annotations.length - 1; @@ -1131,6 +1149,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; + case 's': case 'S': // Stem case for RNA secondary structure drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); @@ -1211,42 +1230,55 @@ public class AnnotationPanel extends JPanel implements MouseListener, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { - g.setColor(STEM_COLOUR); + g.setColor(STEM_COLOUR); int sCol = (lastSSX / av.charWidth) + startRes; int x1 = lastSSX; int x2 = (x * av.charWidth); Regex closeparen = new Regex("(\\))"); - String dc=""; + String dc = column == 0 ? "" + : row.annotations[column - 1].displayCharacter; + + boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null + || !dc.equals(row.annotations[sCol - 1].displayCharacter); + boolean diffdownstream = !validRes || !validEnd + || row.annotations[column] == null + || !dc.equals(row.annotations[column].displayCharacter); + // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); // If a closing base pair half of the stem, display a backward arrow - if (column>0 && closeparen.search(dc=row.annotations[column - 1].displayCharacter)) + if (column > 0 && closeparen.search(dc)) { - if (sCol == 0 || row.annotations[sCol - 1] == null - || !dc.equals(row.annotations[sCol - 1].displayCharacter)) - //if (validRes && column>1 && row.annotations[column-2]!=null && dc.equals(row.annotations[column-2].displayCharacter)) - { g.fillPolygon(new int[] - { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); - x1+=5; + if (diffupstream) + // if (validRes && column>1 && row.annotations[column-2]!=null && + // dc.equals(row.annotations[column-2].displayCharacter)) + { + g.fillPolygon(new int[] + { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + x1 += 5; + } + if (diffdownstream) + { + x2 -= 1; } } else { // display a forward arrow - if (!validRes || row.annotations[column] == null - || !dc.equals(row.annotations[column].displayCharacter)) + if (diffdownstream) { - g.fillPolygon( - new int[] - { x2 - 5, x2 - 5, - x2 }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, - 3); - x2-=5; + g.fillPolygon(new int[] + { x2 - 5, x2 - 5, x2 }, new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + x2 -= 5; + } + if (diffupstream) + { + x1 += 1; } } // draw arrow body - g.fillRect(x1, y + 4 + iconOffset, x2-x1, 7); + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); } private void drawGlyphLine(Graphics g, AlignmentAnnotation row, @@ -1254,7 +1286,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, int column, boolean validRes, boolean validEnd) { g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - lastSSX, 2); + g + .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); } private void drawSheetAnnot(Graphics g, AlignmentAnnotation row, @@ -1295,27 +1329,33 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (MAC) { - int ofs=av.charWidth/2; + int ofs = av.charWidth / 2; // Off by 1 offset when drawing rects and ovals // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2-x1, 8, 8, 8); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); if (sCol == 0 || row.annotations[sCol - 1] == null || row.annotations[sCol - 1].secondaryStructure != 'H') { - } else { -// g.setColor(Color.orange); - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2-x1-ofs+1, 8, 0, 0); } - if (!validRes || row.annotations[column] == null + else + { + // g.setColor(Color.orange); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, + 0, 0); + } + if (!validRes || row.annotations[column] == null || row.annotations[column].secondaryStructure != 'H') { - - } else { -// g.setColor(Color.magenta); - g.fillRoundRect(lastSSX+ofs, y + 4 + iconOffset, x2-x1-ofs+1, 8, 0, 0); - + + } + else + { + // g.setColor(Color.magenta); + g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + + 1, 8, 0, 0); + } - + return; } @@ -1326,7 +1366,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, x1 += av.charWidth / 2; } - if (!validRes || row.annotations[column] == null + if (!validRes || row.annotations[column] == null || row.annotations[column].secondaryStructure != 'H') { g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + iconOffset, @@ -1337,7 +1377,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } -public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, + public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight) { if (sRes > aa.annotations.length) @@ -1511,46 +1551,77 @@ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, // draw profile if available if (renderProfile && aa.annotations[column].value != 0) { + int profl[] = getProfileFor(aa, column); - int ht = y1, htn = y2 - y1;// aa.graphHeight; - float wdth; - double ht2 = 0; - char[] dc = new char[1]; - LineMetrics lm; - for (int c = 1; profl != null && c < profl[0];) + // just try to draw the logo if profl is not null + if (profl != null) { - dc[0] = (char) profl[c++]; - wdth = av.charWidth; - wdth /= (float) fm.charsWidth(dc, 0, 1); - if (c > 2) + int ht = y1, htn = y2 - y1;// aa.graphHeight; + float wdth; + double ht2 = 0; + char[] dc; + + /** + * profl.length == 51 indicates that the profile of a secondary + * structure conservation row was accesed. + * Therefore dc gets length 2, to have space for a basepair instead of + * just a single nucleotide + */ + if (profl.length == 51) + { + dc = new char[2]; + } + else { - ht += (int) ht2; + dc = new char[1]; } + + LineMetrics lm; + for (int c = 1; profl != null && c < profl[0];) { - // if (aa.annotations[column].value==0) { - // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, - // (ht2=(aa.graphHeight*0.1/av.charHeight))))); - // ht = y2-(int)ht2; - // } else { - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) - / av.charHeight))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - // htn -=ht2; - // } - g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) - // ? );// try to get a - // colourscheme for the - // group(aa.groupRef.cs==null) - // ? av.textColour2 : - // cs.findColour(dc)); - g.drawChars(dc, 0, 1, x * av.charWidth, - (int) (ht + lm.getHeight())); - // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); + dc[0] = (char) profl[c++]; + + if (aa.label.startsWith("StrucConsensus")) + { + dc[1] = (char) profl[c++]; + } + + wdth = av.charWidth; + wdth /= (float) fm.charsWidth(dc, 0, dc.length); + + if (c > 2) + { + ht += (int) ht2; + } + { + // if (aa.annotations[column].value==0) { + // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, + // (ht2=(aa.graphHeight*0.1/av.charHeight))))); + // ht = y2-(int)ht2; + // } else { + g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( + wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) + / av.charHeight))); + lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); + // htn -=ht2; + // } + g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) + // ? );// try to get a + // colourscheme for the + // group(aa.groupRef.cs==null) + // ? av.textColour2 : + // cs.findColour(dc)); + // System.out.println(dc[0]); + + g.drawChars(dc, 0, dc.length, x * av.charWidth, + (int) (ht + lm.getHeight())); + + // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); + } } + g.setFont(ofont); } - g.setFont(ofont); } x++; } @@ -1576,16 +1647,39 @@ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, && aa.groupRef.isShowSequenceLogo()) { return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], - aa.groupRef.getIgnoreGapsConsensus()); + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to // be stored if (aa.groupRef == null && aa.sequenceRef == null && av.isShowSequenceLogo()) { - return AAFrequency.extractProfile(av.hconsensus[column], - av.getIgnoreGapsConsensus()); + return AAFrequency.extractProfile(av.hconsensus[column], av + .getIgnoreGapsConsensus()); + } + } + else + { + if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) + { + if (aa.groupRef != null && aa.groupRef.consensusData != null + && aa.groupRef.isShowSequenceLogo()) + { + //TODO check what happens for group selections + return StructureFrequency.extractProfile( + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus()); + } + // TODO extend annotation row to enable dynamic and static profile data + // to + // be stored + if (aa.groupRef == null && aa.sequenceRef == null + && av.isShowSequenceLogo()) + { + return StructureFrequency.extractProfile(av.hStrucConsensus[column], + av.getIgnoreGapsConsensus()); + } } } return null;