-Clazz.declarePackage ("jalview.appletgui");\r
-Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["jalview.util.Comparison", "java.awt.Color", "$.Font"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.av = null;\r
-this.fm = null;\r
-this.renderGaps = true;\r
-this.currentSequenceGroup = null;\r
-this.allGroups = null;\r
-this.resBoxColour = null;\r
-this.graphics = null;\r
-this.forOverview = false;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.appletgui, "SequenceRenderer", null, jalview.api.SequenceRenderer);\r
-Clazz.makeConstructor (c$, \r
-function (av) {\r
-this.av = av;\r
-}, "jalview.appletgui.AlignViewport");\r
-Clazz.defineMethod (c$, "prepare", \r
-function (g, renderGaps) {\r
-this.graphics = g;\r
-this.fm = g.getFontMetrics ();\r
-this.renderGaps = renderGaps;\r
-}, "java.awt.Graphics,~B");\r
-Clazz.overrideMethod (c$, "getResidueBoxColour", \r
-function (seq, i) {\r
-this.allGroups = this.av.getAlignment ().findAllGroups (seq);\r
-if (this.inCurrentSequenceGroup (i)) {\r
-if (this.currentSequenceGroup.getDisplayBoxes ()) {\r
-this.getBoxColour (this.currentSequenceGroup.cs, seq, i);\r
-}} else if (this.av.getShowBoxes ()) {\r
-this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);\r
-}return this.resBoxColour;\r
-}, "jalview.datamodel.SequenceI,~N");\r
-Clazz.overrideMethod (c$, "getResidueColour", \r
-function (seq, position, fr) {\r
-var col = this.getResidueBoxColour (seq, position);\r
-if (fr != null) {\r
-col = fr.findFeatureColour (col, seq, position);\r
-}return col;\r
-}, "jalview.datamodel.SequenceI,~N,jalview.api.FeatureRenderer");\r
-Clazz.defineMethod (c$, "getBoxColour", \r
-function (cs, seq, i) {\r
-if (cs != null) {\r
-this.resBoxColour = cs.findColour (seq.getCharAt (i), i, seq);\r
-} else if (this.forOverview && !jalview.util.Comparison.isGap (seq.getCharAt (i))) {\r
-this.resBoxColour = java.awt.Color.lightGray;\r
-} else {\r
-this.resBoxColour = java.awt.Color.white;\r
-}}, "jalview.schemes.ColourSchemeI,jalview.datamodel.SequenceI,~N");\r
-Clazz.defineMethod (c$, "findSequenceColour", \r
-function (seq, i) {\r
-this.allGroups = this.av.getAlignment ().findAllGroups (seq);\r
-this.drawBoxes (seq, i, i, 0);\r
-return this.resBoxColour;\r
-}, "jalview.datamodel.SequenceI,~N");\r
-Clazz.defineMethod (c$, "drawSequence", \r
-function (seq, sg, start, end, y1) {\r
-if (seq == null) {\r
-return;\r
-}this.allGroups = sg;\r
-this.drawBoxes (seq, start, end, y1);\r
-if (this.av.validCharWidth) {\r
-this.drawText (seq, start, end, y1);\r
-}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N");\r
-Clazz.defineMethod (c$, "drawBoxes", \r
-function (seq, start, end, y1) {\r
-var i = start;\r
-var length = seq.getLength ();\r
-var curStart = -1;\r
-var curWidth = this.av.getCharWidth ();\r
-var avCharWidth = this.av.getCharWidth ();\r
-var avCharHeight = this.av.getCharHeight ();\r
-var tempColour = null;\r
-while (i <= end) {\r
-this.resBoxColour = java.awt.Color.white;\r
-if (i < length) {\r
-if (this.inCurrentSequenceGroup (i)) {\r
-if (this.currentSequenceGroup.getDisplayBoxes ()) {\r
-this.getBoxColour (this.currentSequenceGroup.cs, seq, i);\r
-}} else if (this.av.getShowBoxes ()) {\r
-this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);\r
-}}if (this.resBoxColour !== tempColour) {\r
-if (tempColour != null) {\r
-this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight);\r
-}this.graphics.setColor (this.resBoxColour);\r
-curStart = i;\r
-curWidth = avCharWidth;\r
-tempColour = this.resBoxColour;\r
-} else {\r
-curWidth += avCharWidth;\r
-}i++;\r
-}\r
-this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight);\r
-}, "jalview.datamodel.SequenceI,~N,~N,~N");\r
-Clazz.defineMethod (c$, "drawText", \r
-function (seq, start, end, y1) {\r
-var avCharWidth = this.av.getCharWidth ();\r
-var avCharHeight = this.av.getCharHeight ();\r
-var boldFont = null;\r
-var bold = false;\r
-if (this.av.isUpperCasebold ()) {\r
-boldFont = new java.awt.Font (this.av.getFont ().getName (), 1, avCharHeight);\r
-this.graphics.setFont (this.av.getFont ());\r
-}y1 += avCharHeight - Clazz.doubleToInt (avCharHeight / 5);\r
-var charOffset = 0;\r
-if (end + 1 >= seq.getLength ()) {\r
-end = seq.getLength () - 1;\r
-}var s = ' ';\r
-var srep = this.av.isDisplayReferenceSeq ();\r
-for (var i = start; i <= end; i++) {\r
-this.graphics.setColor (java.awt.Color.black);\r
-s = seq.getCharAt (i);\r
-if (!this.renderGaps && jalview.util.Comparison.isGap (s)) {\r
-continue;\r
-}if (this.inCurrentSequenceGroup (i)) {\r
-if (!this.currentSequenceGroup.getDisplayText ()) {\r
-continue;\r
-}if (this.currentSequenceGroup.getColourText ()) {\r
-this.getBoxColour (this.currentSequenceGroup.cs, seq, i);\r
-this.graphics.setColor (this.resBoxColour.darker ());\r
-}if (this.currentSequenceGroup.getShowNonconserved ()) {\r
-s = this.getDisplayChar (srep, i, s, '.');\r
-}} else {\r
-if (!this.av.getShowText ()) {\r
-continue;\r
-}if (this.av.getColourText ()) {\r
-this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);\r
-if (this.av.getShowBoxes ()) {\r
-this.graphics.setColor (this.resBoxColour.darker ());\r
-} else {\r
-this.graphics.setColor (this.resBoxColour);\r
-}}if (this.av.getShowUnconserved ()) {\r
-s = this.getDisplayChar (srep, i, s, '.');\r
-}}if (this.av.isUpperCasebold ()) {\r
-this.fm = this.graphics.getFontMetrics ();\r
-if ('A' <= s && s <= 'Z') {\r
-if (!bold) {\r
-this.graphics.setFont (boldFont);\r
-}bold = true;\r
-} else if (bold) {\r
-this.graphics.setFont (this.av.font);\r
-bold = false;\r
-}}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2);\r
-this.graphics.drawString (String.valueOf (s), charOffset + avCharWidth * (i - start), y1);\r
-}\r
-}, "jalview.datamodel.SequenceI,~N,~N,~N");\r
-Clazz.defineMethod (c$, "getDisplayChar", \r
- function (usesrep, position, s, c) {\r
-var conschar = (usesrep) ? this.av.getAlignment ().getSeqrep ().getCharAt (position) : this.av.getAlignmentConsensusAnnotation ().annotations[position].displayCharacter.charAt (0);\r
-if (conschar != '-' && s == conschar) {\r
-s = c;\r
-}return s;\r
-}, "~B,~N,~S,~S");\r
-Clazz.defineMethod (c$, "inCurrentSequenceGroup", \r
-function (res) {\r
-if (this.allGroups == null) {\r
-return false;\r
-}for (var i = 0; i < this.allGroups.length; i++) {\r
-if (this.allGroups[i].getStartRes () <= res && this.allGroups[i].getEndRes () >= res) {\r
-this.currentSequenceGroup = this.allGroups[i];\r
-return true;\r
-}}\r
-return false;\r
-}, "~N");\r
-Clazz.defineMethod (c$, "drawHighlightedText", \r
-function (seq, start, end, x1, y1) {\r
-var avCharWidth = this.av.getCharWidth ();\r
-var avCharHeight = this.av.getCharHeight ();\r
-var pady = Clazz.doubleToInt (avCharHeight / 5);\r
-var charOffset = 0;\r
-this.graphics.setColor (java.awt.Color.black);\r
-this.graphics.fillRect (x1, y1, avCharWidth * (end - start + 1), avCharHeight);\r
-this.graphics.setColor (java.awt.Color.white);\r
-var s = '~';\r
-if (this.av.validCharWidth) {\r
-for (var i = start; i <= end; i++) {\r
-if (i < seq.getLength ()) {\r
-s = seq.getCharAt (i);\r
-}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2);\r
-this.graphics.drawString (String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady);\r
-}\r
-}}, "jalview.datamodel.SequenceI,~N,~N,~N,~N");\r
-Clazz.defineMethod (c$, "drawCursor", \r
-function (seq, res, x1, y1) {\r
-var pady = Clazz.doubleToInt (this.av.getCharHeight () / 5);\r
-var charOffset = 0;\r
-this.graphics.setColor (java.awt.Color.black);\r
-this.graphics.fillRect (x1, y1, this.av.getCharWidth (), this.av.getCharHeight ());\r
-this.graphics.setColor (java.awt.Color.white);\r
-this.graphics.setColor (java.awt.Color.white);\r
-var s = seq.getCharAt (res);\r
-if (this.av.validCharWidth) {\r
-charOffset = Clazz.doubleToInt ((this.av.getCharWidth () - this.fm.charWidth (s)) / 2);\r
-this.graphics.drawString (String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady);\r
-}}, "jalview.datamodel.SequenceI,~N,~N,~N");\r
-});\r
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["jalview.api.SequenceRenderer"], "jalview.appletgui.SequenceRenderer", ["jalview.util.Comparison", "java.awt.Color", "$.Font"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.av = null;
+this.fm = null;
+this.renderGaps = true;
+this.currentSequenceGroup = null;
+this.allGroups = null;
+this.resBoxColour = null;
+this.graphics = null;
+this.forOverview = false;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "SequenceRenderer", null, jalview.api.SequenceRenderer);
+Clazz.makeConstructor (c$,
+function (av) {
+this.av = av;
+}, "jalview.appletgui.AlignViewport");
+Clazz.defineMethod (c$, "prepare",
+function (g, renderGaps) {
+this.graphics = g;
+this.fm = g.getFontMetrics ();
+this.renderGaps = renderGaps;
+}, "java.awt.Graphics,~B");
+Clazz.overrideMethod (c$, "getResidueBoxColour",
+function (seq, i) {
+this.allGroups = this.av.getAlignment ().findAllGroups (seq);
+if (this.inCurrentSequenceGroup (i)) {
+if (this.currentSequenceGroup.getDisplayBoxes ()) {
+this.getBoxColour (this.currentSequenceGroup.cs, seq, i);
+}} else if (this.av.getShowBoxes ()) {
+this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);
+}return this.resBoxColour;
+}, "jalview.datamodel.SequenceI,~N");
+Clazz.overrideMethod (c$, "getResidueColour",
+function (seq, position, fr) {
+var col = this.getResidueBoxColour (seq, position);
+if (fr != null) {
+col = fr.findFeatureColour (col, seq, position);
+}return col;
+}, "jalview.datamodel.SequenceI,~N,jalview.api.FeatureRenderer");
+Clazz.defineMethod (c$, "getBoxColour",
+function (cs, seq, i) {
+if (cs != null) {
+this.resBoxColour = cs.findColour (seq.getCharAt (i), i, seq);
+} else if (this.forOverview && !jalview.util.Comparison.isGap (seq.getCharAt (i))) {
+this.resBoxColour = java.awt.Color.lightGray;
+} else {
+this.resBoxColour = java.awt.Color.white;
+}}, "jalview.schemes.ColourSchemeI,jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "findSequenceColour",
+function (seq, i) {
+this.allGroups = this.av.getAlignment ().findAllGroups (seq);
+this.drawBoxes (seq, i, i, 0);
+return this.resBoxColour;
+}, "jalview.datamodel.SequenceI,~N");
+Clazz.defineMethod (c$, "drawSequence",
+function (seq, sg, start, end, y1) {
+if (seq == null) {
+return;
+}this.allGroups = sg;
+this.drawBoxes (seq, start, end, y1);
+if (this.av.validCharWidth) {
+this.drawText (seq, start, end, y1);
+}}, "jalview.datamodel.SequenceI,~A,~N,~N,~N");
+Clazz.defineMethod (c$, "drawBoxes",
+function (seq, start, end, y1) {
+var i = start;
+var length = seq.getLength ();
+var curStart = -1;
+var curWidth = this.av.getCharWidth ();
+var avCharWidth = this.av.getCharWidth ();
+var avCharHeight = this.av.getCharHeight ();
+var tempColour = null;
+while (i <= end) {
+this.resBoxColour = java.awt.Color.white;
+if (i < length) {
+if (this.inCurrentSequenceGroup (i)) {
+if (this.currentSequenceGroup.getDisplayBoxes ()) {
+this.getBoxColour (this.currentSequenceGroup.cs, seq, i);
+}} else if (this.av.getShowBoxes ()) {
+this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);
+}}if (this.resBoxColour !== tempColour) {
+if (tempColour != null) {
+this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight);
+}this.graphics.setColor (this.resBoxColour);
+curStart = i;
+curWidth = avCharWidth;
+tempColour = this.resBoxColour;
+} else {
+curWidth += avCharWidth;
+}i++;
+}
+this.graphics.fillRect (avCharWidth * (curStart - start), y1, curWidth, avCharHeight);
+}, "jalview.datamodel.SequenceI,~N,~N,~N");
+Clazz.defineMethod (c$, "drawText",
+function (seq, start, end, y1) {
+var avCharWidth = this.av.getCharWidth ();
+var avCharHeight = this.av.getCharHeight ();
+var boldFont = null;
+var bold = false;
+if (this.av.isUpperCasebold ()) {
+boldFont = new java.awt.Font (this.av.getFont ().getName (), 1, avCharHeight);
+this.graphics.setFont (this.av.getFont ());
+}y1 += avCharHeight - Clazz.doubleToInt (avCharHeight / 5);
+var charOffset = 0;
+if (end + 1 >= seq.getLength ()) {
+end = seq.getLength () - 1;
+}var s = ' ';
+var srep = this.av.isDisplayReferenceSeq ();
+for (var i = start; i <= end; i++) {
+this.graphics.setColor (java.awt.Color.black);
+s = seq.getCharAt (i);
+if (!this.renderGaps && jalview.util.Comparison.isGap (s)) {
+continue;
+}if (this.inCurrentSequenceGroup (i)) {
+if (!this.currentSequenceGroup.getDisplayText ()) {
+continue;
+}if (this.currentSequenceGroup.getColourText ()) {
+this.getBoxColour (this.currentSequenceGroup.cs, seq, i);
+this.graphics.setColor (this.resBoxColour.darker ());
+}if (this.currentSequenceGroup.getShowNonconserved ()) {
+s = this.getDisplayChar (srep, i, s, '.');
+}} else {
+if (!this.av.getShowText ()) {
+continue;
+}if (this.av.getColourText ()) {
+this.getBoxColour (this.av.getGlobalColourScheme (), seq, i);
+if (this.av.getShowBoxes ()) {
+this.graphics.setColor (this.resBoxColour.darker ());
+} else {
+this.graphics.setColor (this.resBoxColour);
+}}if (this.av.getShowUnconserved ()) {
+s = this.getDisplayChar (srep, i, s, '.');
+}}if (this.av.isUpperCasebold ()) {
+this.fm = this.graphics.getFontMetrics ();
+if ('A' <= s && s <= 'Z') {
+if (!bold) {
+this.graphics.setFont (boldFont);
+}bold = true;
+} else if (bold) {
+this.graphics.setFont (this.av.font);
+bold = false;
+}}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2);
+this.graphics.drawString (String.valueOf (s), charOffset + avCharWidth * (i - start), y1);
+}
+}, "jalview.datamodel.SequenceI,~N,~N,~N");
+Clazz.defineMethod (c$, "getDisplayChar",
+ function (usesrep, position, s, c) {
+var conschar = (usesrep) ? this.av.getAlignment ().getSeqrep ().getCharAt (position) : this.av.getAlignmentConsensusAnnotation ().annotations[position].displayCharacter.charAt (0);
+if (conschar != '-' && s == conschar) {
+s = c;
+}return s;
+}, "~B,~N,~S,~S");
+Clazz.defineMethod (c$, "inCurrentSequenceGroup",
+function (res) {
+if (this.allGroups == null) {
+return false;
+}for (var i = 0; i < this.allGroups.length; i++) {
+if (this.allGroups[i].getStartRes () <= res && this.allGroups[i].getEndRes () >= res) {
+this.currentSequenceGroup = this.allGroups[i];
+return true;
+}}
+return false;
+}, "~N");
+Clazz.defineMethod (c$, "drawHighlightedText",
+function (seq, start, end, x1, y1) {
+var avCharWidth = this.av.getCharWidth ();
+var avCharHeight = this.av.getCharHeight ();
+var pady = Clazz.doubleToInt (avCharHeight / 5);
+var charOffset = 0;
+this.graphics.setColor (java.awt.Color.black);
+this.graphics.fillRect (x1, y1, avCharWidth * (end - start + 1), avCharHeight);
+this.graphics.setColor (java.awt.Color.white);
+var s = '~';
+if (this.av.validCharWidth) {
+for (var i = start; i <= end; i++) {
+if (i < seq.getLength ()) {
+s = seq.getCharAt (i);
+}charOffset = Clazz.doubleToInt ((avCharWidth - this.fm.charWidth (s)) / 2);
+this.graphics.drawString (String.valueOf (s), charOffset + x1 + avCharWidth * (i - start), y1 + avCharHeight - pady);
+}
+}}, "jalview.datamodel.SequenceI,~N,~N,~N,~N");
+Clazz.defineMethod (c$, "drawCursor",
+function (seq, res, x1, y1) {
+var pady = Clazz.doubleToInt (this.av.getCharHeight () / 5);
+var charOffset = 0;
+this.graphics.setColor (java.awt.Color.black);
+this.graphics.fillRect (x1, y1, this.av.getCharWidth (), this.av.getCharHeight ());
+this.graphics.setColor (java.awt.Color.white);
+this.graphics.setColor (java.awt.Color.white);
+var s = seq.getCharAt (res);
+if (this.av.validCharWidth) {
+charOffset = Clazz.doubleToInt ((this.av.getCharWidth () - this.fm.charWidth (s)) / 2);
+this.graphics.drawString (String.valueOf (s), charOffset + x1, (y1 + this.av.getCharHeight ()) - pady);
+}}, "jalview.datamodel.SequenceI,~N,~N,~N");
+});
git://source.jalview.org / jalviewjs.git / blobdiff