-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.structure.SequenceListener;\r
-import jalview.structure.StructureSelectionManager;\r
-\r
-public class SeqPanel\r
- extends Panel implements MouseMotionListener, MouseListener, SequenceListener\r
-{\r
-\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
-\r
- protected int lastres;\r
- protected int startseq;\r
-\r
- protected AlignViewport av;\r
-\r
- // if character is inserted or deleted, we will need to recalculate the conservation\r
- boolean seqEditOccurred = false;\r
-\r
- ScrollThread scrollThread = null;\r
- boolean mouseDragging = false;\r
- boolean editingSeqs = false;\r
- boolean groupEditing = false;\r
-\r
- int oldSeq = -1;\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
-\r
- StringBuffer keyboardNo1;\r
- StringBuffer keyboardNo2;\r
-\r
- boolean mouseWheelPressed = false;\r
- Point lastMousePress;\r
-\r
- EditCommand editCommand;\r
-\r
- StructureSelectionManager ssm;\r
-\r
-\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
- {\r
- this.av = avp;\r
-\r
- seqCanvas = new SeqCanvas(avp);\r
- setLayout(new BorderLayout());\r
- add(seqCanvas);\r
-\r
- ap = p;\r
-\r
- seqCanvas.addMouseMotionListener(this);\r
- seqCanvas.addMouseListener(this);\r
- ssm = StructureSelectionManager.getStructureSelectionManager();\r
- ssm.addStructureViewerListener(this);\r
-\r
- seqCanvas.repaint();\r
- }\r
-\r
- void endEditing()\r
- {\r
- if (editCommand != null && editCommand.getSize() > 0)\r
- {\r
- ap.alignFrame.addHistoryItem(editCommand);\r
- av.firePropertyChange("alignment", null,\r
- av.getAlignment().getSequences());\r
- }\r
-\r
- startseq = -1;\r
- lastres = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
- keyboardNo1 = null;\r
- keyboardNo2 = null;\r
- editCommand = null;\r
- }\r
-\r
- void setCursorRow()\r
- {\r
- seqCanvas.cursorY = getKeyboardNo1() - 1;\r
- scrollToVisible();\r
- }\r
-\r
- void setCursorColumn()\r
- {\r
- seqCanvas.cursorX = getKeyboardNo1() - 1;\r
- scrollToVisible();\r
- }\r
-\r
- void setCursorRowAndColumn()\r
- {\r
- if (keyboardNo2 == null)\r
- {\r
- keyboardNo2 = new StringBuffer();\r
- }\r
- else\r
- {\r
- seqCanvas.cursorX = getKeyboardNo1() - 1;\r
- seqCanvas.cursorY = getKeyboardNo2() - 1;\r
- scrollToVisible();\r
- }\r
- }\r
-\r
- void setCursorPosition()\r
- {\r
- SequenceI sequence =\r
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
-\r
- seqCanvas.cursorX = sequence.findIndex(\r
- getKeyboardNo1() - 1\r
- );\r
- scrollToVisible();\r
- }\r
-\r
- void moveCursor(int dx, int dy)\r
- {\r
- seqCanvas.cursorX += dx;\r
- seqCanvas.cursorY += dy;\r
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))\r
- {\r
- int original = seqCanvas.cursorX - dx;\r
- int maxWidth = av.alignment.getWidth();\r
-\r
- while (!av.colSel.isVisible(seqCanvas.cursorX)\r
- && seqCanvas.cursorX < maxWidth\r
- && seqCanvas.cursorX > 0)\r
- {\r
- seqCanvas.cursorX += dx;\r
- }\r
-\r
- if (seqCanvas.cursorX >= maxWidth\r
- || !av.colSel.isVisible(seqCanvas.cursorX))\r
- {\r
- seqCanvas.cursorX = original;\r
- }\r
- }\r
- scrollToVisible();\r
- }\r
-\r
- void scrollToVisible()\r
- {\r
- if (seqCanvas.cursorX < 0)\r
- {\r
- seqCanvas.cursorX = 0;\r
- }\r
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)\r
- {\r
- seqCanvas.cursorX = av.alignment.getWidth() - 1;\r
- }\r
-\r
- if (seqCanvas.cursorY < 0)\r
- {\r
- seqCanvas.cursorY = 0;\r
- }\r
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)\r
- {\r
- seqCanvas.cursorY = av.alignment.getHeight() - 1;\r
- }\r
-\r
- endEditing();\r
- if (av.wrapAlignment)\r
- {\r
- ap.scrollToWrappedVisible(seqCanvas.cursorX);\r
- }\r
- else\r
- {\r
- while (seqCanvas.cursorY < av.startSeq)\r
- {\r
- ap.scrollUp(true);\r
- }\r
- while (seqCanvas.cursorY + 1 > av.endSeq)\r
- {\r
- ap.scrollUp(false);\r
- }\r
- while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))\r
- {\r
-\r
- if (!ap.scrollRight(false))\r
- {\r
- break;\r
- }\r
- }\r
- while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))\r
- {\r
- if (!ap.scrollRight(true))\r
- {\r
- break;\r
- }\r
- }\r
- }\r
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),\r
- seqCanvas.cursorX, seqCanvas.cursorY);\r
-\r
- seqCanvas.repaint();\r
- }\r
-\r
- void setSelectionAreaAtCursor(boolean topLeft)\r
- {\r
- SequenceI sequence =\r
- (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);\r
-\r
- if (av.getSelectionGroup() != null)\r
- {\r
- SequenceGroup sg = av.selectionGroup;\r
- //Find the top and bottom of this group\r
- int min = av.alignment.getHeight(), max = 0;\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- int index = av.alignment.findIndex(sg.getSequenceAt(i));\r
- if (index > max)\r
- {\r
- max = index;\r
- }\r
- if (index < min)\r
- {\r
- min = index;\r
- }\r
- }\r
-\r
- max++;\r
-\r
- if (topLeft)\r
- {\r
- sg.setStartRes(seqCanvas.cursorX);\r
- if (sg.getEndRes() < seqCanvas.cursorX)\r
- {\r
- sg.setEndRes(seqCanvas.cursorX);\r
- }\r
-\r
- min = seqCanvas.cursorY;\r
- }\r
- else\r
- {\r
- sg.setEndRes(seqCanvas.cursorX);\r
- if (sg.getStartRes() > seqCanvas.cursorX)\r
- {\r
- sg.setStartRes(seqCanvas.cursorX);\r
- }\r
-\r
- max = seqCanvas.cursorY + 1;\r
- }\r
-\r
- if (min > max)\r
- {\r
- // Only the user can do this\r
- av.setSelectionGroup(null);\r
- }\r
- else\r
- {\r
- // Now add any sequences between min and max\r
- sg.getSequences(null).removeAllElements();\r
- for (int i = min; i < max; i++)\r
- {\r
- sg.addSequence(av.alignment.getSequenceAt(i), false);\r
- }\r
- }\r
- }\r
-\r
- if (av.getSelectionGroup() == null)\r
- {\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(seqCanvas.cursorX);\r
- sg.setEndRes(seqCanvas.cursorX);\r
- sg.addSequence(sequence, false);\r
- av.setSelectionGroup(sg);\r
- }\r
-\r
- ap.paintAlignment(false);\r
- }\r
-\r
- void insertGapAtCursor(boolean group)\r
- {\r
- groupEditing = group;\r
- startseq = seqCanvas.cursorY;\r
- lastres = seqCanvas.cursorX;\r
- editSequence(true, seqCanvas.cursorX + getKeyboardNo1());\r
- endEditing();\r
- }\r
-\r
- void deleteGapAtCursor(boolean group)\r
- {\r
- groupEditing = group;\r
- startseq = seqCanvas.cursorY;\r
- lastres = seqCanvas.cursorX + getKeyboardNo1();\r
- editSequence(false, seqCanvas.cursorX);\r
- endEditing();\r
- }\r
-\r
- void numberPressed(char value)\r
- {\r
- if (keyboardNo1 == null)\r
- {\r
- keyboardNo1 = new StringBuffer();\r
- }\r
-\r
- if (keyboardNo2 != null)\r
- {\r
- keyboardNo2.append(value);\r
- }\r
- else\r
- {\r
- keyboardNo1.append(value);\r
- }\r
- }\r
-\r
- int getKeyboardNo1()\r
- {\r
- if (keyboardNo1 == null)\r
- return 1;\r
- else\r
- {\r
- int value = Integer.parseInt(keyboardNo1.toString());\r
- keyboardNo1 = null;\r
- return value;\r
- }\r
- }\r
-\r
- int getKeyboardNo2()\r
- {\r
- if (keyboardNo2 == null)\r
- return 1;\r
- else\r
- {\r
- int value = Integer.parseInt(keyboardNo2.toString());\r
- keyboardNo2 = null;\r
- return value;\r
- }\r
- }\r
-\r
-\r
- void setStatusMessage(SequenceI sequence, int res, int seq)\r
- {\r
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
- sequence.getName());\r
-\r
- Object obj = null;\r
- if (av.alignment.isNucleotide())\r
- {\r
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
- "");\r
- if (obj != null)\r
- {\r
- text.append(" Nucleotide: ");\r
- }\r
- }\r
- else\r
- {\r
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
- if (obj != null)\r
- {\r
- text.append(" Residue: ");\r
- }\r
- }\r
-\r
- if (obj != null)\r
- {\r
-\r
- if (obj != "")\r
- {\r
- text.append(obj + " (" + sequence.findPosition(res) +\r
- ")");\r
- }\r
- }\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- lastMousePress = evt.getPoint();\r
-\r
- //For now, ignore the mouseWheel font resizing on Macs\r
- //As the Button2_mask always seems to be true\r
- if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==\r
- InputEvent.BUTTON2_MASK && !av.MAC)\r
- {\r
- mouseWheelPressed = true;\r
- return;\r
- }\r
-\r
- if (evt.isShiftDown()\r
- || evt.isControlDown()\r
- || evt.isAltDown())\r
- {\r
- if (evt.isControlDown() || evt.isAltDown())\r
- {\r
- groupEditing = true;\r
- }\r
- editingSeqs = true;\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- return;\r
- }\r
-\r
- int seq = findSeq(evt);\r
- int res = findRes(evt);\r
-\r
- if (seq < 0 || res < 0)\r
- {\r
- return;\r
- }\r
-\r
- if ( (seq < av.getAlignment().getHeight()) &&\r
- (res < av.getAlignment().getSequenceAt(seq).getLength()))\r
- {\r
- startseq = seq;\r
- lastres = res;\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- lastres = -1;\r
- }\r
-\r
- return;\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));\r
- if (evt.getClickCount() > 1)\r
- {\r
- if (av.getSelectionGroup().getSize() == 1\r
- && av.getSelectionGroup().getEndRes()\r
- - av.getSelectionGroup().getStartRes() < 2)\r
- {\r
- av.setSelectionGroup(null);\r
- }\r
-\r
- SequenceFeature[] features = findFeaturesAtRes(\r
- sequence,\r
- sequence.findPosition(findRes(evt))\r
- );\r
-\r
- if (features != null && features.length > 0)\r
- {\r
- SearchResults highlight = new SearchResults();\r
- highlight.addResult(sequence,\r
- features[0].getBegin(),\r
- features[0].getEnd());\r
- seqCanvas.highlightSearchResults(highlight);\r
- }\r
- if (features != null && features.length > 0)\r
- {\r
- seqCanvas.getFeatureRenderer().amendFeatures(\r
- new SequenceI[]\r
- {sequence}, features, false, ap);\r
-\r
- seqCanvas.highlightSearchResults(null);\r
- }\r
- }\r
- }\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- mouseDragging = false;\r
- mouseWheelPressed = false;\r
- ap.paintAlignment(true);\r
-\r
- if (!editingSeqs)\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- return;\r
- }\r
-\r
- endEditing();\r
-\r
- }\r
-\r
- int startWrapBlock = -1;\r
- int wrappedBlock = -1;\r
- int findRes(MouseEvent evt)\r
- {\r
- int res = 0;\r
- int x = evt.getX();\r
-\r
- if (av.wrapAlignment)\r
- {\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- {\r
- hgap += av.charHeight;\r
- }\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap + seqCanvas.getAnnotationHeight();\r
-\r
- int y = evt.getY();\r
- y -= hgap;\r
- x -= seqCanvas.LABEL_WEST;\r
-\r
- int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);\r
- if (cwidth < 1)\r
- {\r
- return 0;\r
- }\r
-\r
- wrappedBlock = y / cHeight;\r
- wrappedBlock += av.getStartRes() / cwidth;\r
-\r
- res = wrappedBlock * cwidth + x / av.getCharWidth();\r
-\r
- }\r
- else\r
- {\r
- res = (x / av.getCharWidth()) + av.getStartRes();\r
- }\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- res = av.getColumnSelection().adjustForHiddenColumns(res);\r
- }\r
-\r
- return res;\r
-\r
- }\r
-\r
- int findSeq(MouseEvent evt)\r
- {\r
-\r
- int seq = 0;\r
- int y = evt.getY();\r
-\r
- if (av.wrapAlignment)\r
- {\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- {\r
- hgap += av.charHeight;\r
- }\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap + seqCanvas.getAnnotationHeight();\r
-\r
- y -= hgap;\r
-\r
- seq = Math.min( (y % cHeight) / av.getCharHeight(),\r
- av.alignment.getHeight() - 1);\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
- }\r
- else\r
- {\r
- seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),\r
- av.alignment.getHeight() - 1);\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
- }\r
-\r
- return seq;\r
- }\r
-\r
-\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
-\r
- int seq = findSeq(evt);\r
- int res = findRes(evt);\r
-\r
- if (seq < av.getAlignment().getHeight() &&\r
- res < av.getAlignment().getSequenceAt(seq).getLength())\r
- {\r
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
- // Find the residue's position in the sequence (res is the position\r
- // in the alignment\r
-\r
- startseq = seq;\r
- lastres = res;\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- lastres = -1;\r
- }\r
-\r
- return;\r
- }\r
-\r
-\r
- String lastMessage;\r
- public void mouseOverSequence(SequenceI sequence, int index)\r
- {\r
- String tmp = sequence.hashCode()+index+"";\r
- if (lastMessage == null || !lastMessage.equals(tmp))\r
- ssm.mouseOverSequence(sequence, index);\r
-\r
- lastMessage = tmp;\r
- }\r
-\r
-\r
- public void highlightSequence(SearchResults results)\r
- {\r
- seqCanvas.highlightSearchResults(results);\r
- }\r
-\r
- public void updateColours(SequenceI seq, int index)\r
- {\r
- System.out.println("update the seqPanel colours");\r
- //repaint();\r
- }\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- int res = findRes(evt);\r
- int seq = findSeq(evt);\r
-\r
- if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)\r
- {\r
- if (tooltip != null)\r
- {\r
- tooltip.setTip("");\r
- }\r
- return;\r
- }\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if (res > sequence.getLength())\r
- {\r
- if (tooltip != null)\r
- {\r
- tooltip.setTip("");\r
- }\r
- return;\r
- }\r
-\r
-\r
- if (ssm != null)\r
- mouseOverSequence(sequence, sequence.findPosition(res));\r
-\r
-\r
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
- sequence.getName());\r
-\r
- Object obj = null;\r
- if (av.alignment.isNucleotide())\r
- {\r
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +\r
- "");\r
- if (obj != null)\r
- {\r
- text.append(" Nucleotide: ");\r
- }\r
- }\r
- else\r
- {\r
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");\r
- if (obj != null)\r
- {\r
- text.append(" Residue: ");\r
- }\r
- }\r
-\r
- if (obj != null)\r
- {\r
- if (obj != "")\r
- {\r
- text.append(obj + " (" + sequence.findPosition(res) + ")");\r
- }\r
- }\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
- StringBuffer tooltipText = new StringBuffer();\r
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);\r
- if (groups != null)\r
- {\r
- for (int g = 0; g < groups.length; g++)\r
- {\r
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)\r
- {\r
- if (!groups[g].getName().startsWith("JTreeGroup") &&\r
- !groups[g].getName().startsWith("JGroup"))\r
- {\r
- tooltipText.append(groups[g].getName() + " ");\r
- }\r
- if (groups[g].getDescription() != null)\r
- {\r
- tooltipText.append(groups[g].getDescription());\r
- }\r
- tooltipText.append("\n");\r
- }\r
- }\r
- }\r
-\r
- // use aa to see if the mouse pointer is on a\r
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,\r
- sequence.findPosition(res));\r
-\r
- int index = 0;\r
- while (index < allFeatures.length)\r
- {\r
- SequenceFeature sf = allFeatures[index];\r
-\r
- tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);\r
-\r
- if (sf.getDescription() != null)\r
- {\r
- tooltipText.append(" " + sf.getDescription());\r
- }\r
-\r
- if (sf.getValue("status") != null)\r
- {\r
- String status = sf.getValue("status").toString();\r
- if (status.length() > 0)\r
- {\r
- tooltipText.append(" (" + sf.getValue("status") + ")");\r
- }\r
- }\r
- tooltipText.append("\n");\r
-\r
- index++;\r
- }\r
-\r
- if (tooltip == null)\r
- {\r
- tooltip = new Tooltip(tooltipText.toString(), seqCanvas);\r
- }\r
- else\r
- {\r
- tooltip.setTip(tooltipText.toString());\r
- }\r
- }\r
-\r
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)\r
- {\r
- Vector tmp = new Vector();\r
- SequenceFeature[] features = sequence.getSequenceFeatures();\r
- if (features != null)\r
- {\r
- for (int i = 0; i < features.length; i++)\r
- {\r
- if (av.featuresDisplayed == null\r
- || !av.featuresDisplayed.containsKey(features[i].getType()))\r
- {\r
- continue;\r
- }\r
-\r
-\r
-\r
- if (features[i].featureGroup != null\r
- && seqCanvas.fr.featureGroups!=null\r
- && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)\r
- && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())\r
- continue;\r
-\r
-\r
- if ( (features[i].getBegin() <= res) &&\r
- (features[i].getEnd() >= res))\r
- {\r
- tmp.addElement(features[i]);\r
- }\r
- }\r
- }\r
-\r
- features = new SequenceFeature[tmp.size()];\r
- tmp.copyInto(features);\r
-\r
- return features;\r
- }\r
-\r
-\r
- Tooltip tooltip;\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if (mouseWheelPressed)\r
- {\r
- int oldWidth = av.charWidth;\r
-\r
- //Which is bigger, left-right or up-down?\r
- if (Math.abs(evt.getY() - lastMousePress.y)\r
- > Math.abs(evt.getX() - lastMousePress.x))\r
- {\r
- int fontSize = av.font.getSize();\r
-\r
- if (evt.getY() < lastMousePress.y && av.charHeight > 1)\r
- {\r
- fontSize--;\r
- }\r
- else if (evt.getY() > lastMousePress.y)\r
- {\r
- fontSize++;\r
- }\r
-\r
- if (fontSize < 1)\r
- {\r
- fontSize = 1;\r
- }\r
-\r
- av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));\r
- av.charWidth = oldWidth;\r
- }\r
- else\r
- {\r
- if (evt.getX() < lastMousePress.x && av.charWidth > 1)\r
- {\r
- av.charWidth--;\r
- }\r
- else if (evt.getX() > lastMousePress.x)\r
- {\r
- av.charWidth++;\r
- }\r
-\r
- if (av.charWidth < 1)\r
- {\r
- av.charWidth = 1;\r
- }\r
- }\r
-\r
- ap.fontChanged();\r
-\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- av.validCharWidth = fm.charWidth('M') <= av.charWidth;\r
-\r
- lastMousePress = evt.getPoint();\r
-\r
- ap.paintAlignment(false);\r
- ap.annotationPanel.image = null;\r
- return;\r
- }\r
-\r
- if (!editingSeqs)\r
- {\r
- doMouseDraggedDefineMode(evt);\r
- return;\r
- }\r
-\r
- int res = findRes(evt);\r
-\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- if ( (lastres == -1) || (lastres == res))\r
- {\r
- return;\r
- }\r
-\r
- if ( (res < av.getAlignment().getWidth()) && (res < lastres))\r
- {\r
- // dragLeft, delete gap\r
- editSequence(false, res);\r
- }\r
- else\r
- {\r
- editSequence(true, res);\r
- }\r
-\r
- mouseDragging = true;\r
- if (scrollThread != null)\r
- {\r
- scrollThread.setEvent(evt);\r
- }\r
-\r
- }\r
-\r
- synchronized void editSequence(boolean insertGap, int startres)\r
- {\r
- int fixedLeft = -1;\r
- int fixedRight = -1;\r
- boolean fixedColumns = false;\r
- SequenceGroup sg = av.getSelectionGroup();\r
-\r
- SequenceI seq = av.alignment.getSequenceAt(startseq);\r
-\r
- if (!groupEditing && av.hasHiddenRows)\r
- {\r
- if (av.hiddenRepSequences != null\r
- && av.hiddenRepSequences.containsKey(seq))\r
- {\r
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
- groupEditing = true;\r
- }\r
- }\r
-\r
- StringBuffer message = new StringBuffer();\r
- if (groupEditing)\r
- {\r
- message.append("Edit group:");\r
- if (editCommand == null)\r
- {\r
- editCommand = new EditCommand("Edit Group");\r
- }\r
- }\r
- else\r
- {\r
- message.append("Edit sequence: " + seq.getName());\r
- String label = seq.getName();\r
- if (label.length() > 10)\r
- {\r
- label = label.substring(0, 10);\r
- }\r
- if (editCommand == null)\r
- {\r
- editCommand = new EditCommand("Edit " + label);\r
- }\r
- }\r
-\r
- if (insertGap)\r
- {\r
- message.append(" insert ");\r
- }\r
- else\r
- {\r
- message.append(" delete ");\r
- }\r
-\r
- message.append(Math.abs(startres - lastres) + " gaps.");\r
- ap.alignFrame.statusBar.setText(message.toString());\r
-\r
- //Are we editing within a selection group?\r
- if (groupEditing\r
- || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))\r
- {\r
- fixedColumns = true;\r
-\r
- //sg might be null as the user may only see 1 sequence,\r
- //but the sequence represents a group\r
- if (sg == null)\r
- {\r
- if (av.hiddenRepSequences == null\r
- || !av.hiddenRepSequences.containsKey(seq))\r
- {\r
- endEditing();\r
- return;\r
- }\r
-\r
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);\r
- }\r
-\r
- fixedLeft = sg.getStartRes();\r
- fixedRight = sg.getEndRes();\r
-\r
- if ( (startres < fixedLeft && lastres >= fixedLeft)\r
- || (startres >= fixedLeft && lastres < fixedLeft)\r
- || (startres > fixedRight && lastres <= fixedRight)\r
- || (startres <= fixedRight && lastres > fixedRight))\r
- {\r
- endEditing();\r
- return;\r
- }\r
-\r
- if (fixedLeft > startres)\r
- {\r
- fixedRight = fixedLeft - 1;\r
- fixedLeft = 0;\r
- }\r
- else if (fixedRight < startres)\r
- {\r
- fixedLeft = fixedRight;\r
- fixedRight = -1;\r
- }\r
- }\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- fixedColumns = true;\r
- int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);\r
- int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);\r
-\r
- if ( (insertGap && startres > y1 && lastres < y1)\r
- || (!insertGap && startres < y2 && lastres > y2))\r
- {\r
- endEditing();\r
- return;\r
- }\r
-\r
- //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");\r
- //Selection spans a hidden region\r
- if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))\r
- {\r
- if (startres >= y2)\r
- {\r
- fixedLeft = y2;\r
- }\r
- else\r
- {\r
- fixedRight = y2 - 1;\r
- }\r
- }\r
- }\r
-\r
- if (groupEditing)\r
- {\r
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);\r
- int g, groupSize = vseqs.size();\r
- SequenceI[] groupSeqs = new SequenceI[groupSize];\r
- for (g = 0; g < groupSeqs.length; g++)\r
- {\r
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);\r
- }\r
-\r
- // drag to right\r
- if (insertGap)\r
- {\r
- //If the user has selected the whole sequence, and is dragging to\r
- // the right, we can still extend the alignment and selectionGroup\r
- if (sg.getStartRes() == 0\r
- && sg.getEndRes() == fixedRight\r
- && sg.getEndRes() == av.alignment.getWidth() - 1\r
- )\r
- {\r
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);\r
- fixedRight = sg.getEndRes();\r
- }\r
-\r
- // Is it valid with fixed columns??\r
- // Find the next gap before the end\r
- // of the visible region boundary\r
- boolean blank = false;\r
- for (fixedRight = fixedRight;\r
- fixedRight > lastres;\r
- fixedRight--)\r
- {\r
- blank = true;\r
-\r
- for (g = 0; g < groupSize; g++)\r
- {\r
- for (int j = 0; j < startres - lastres; j++)\r
- {\r
- if (!jalview.util.Comparison.isGap(\r
- groupSeqs[g].getCharAt(fixedRight - j)))\r
- {\r
- blank = false;\r
- break;\r
- }\r
- }\r
- }\r
- if (blank)\r
- {\r
- break;\r
- }\r
- }\r
-\r
- if (!blank)\r
- {\r
- if (sg.getSize() == av.alignment.getHeight())\r
- {\r
- if ( (av.hasHiddenColumns\r
- &&\r
- startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))\r
- {\r
- endEditing();\r
- return;\r
- }\r
-\r
- int alWidth = av.alignment.getWidth();\r
- if (av.hasHiddenRows)\r
- {\r
- int hwidth = av.alignment.getHiddenSequences().getWidth();\r
- if (hwidth > alWidth)\r
- {\r
- alWidth = hwidth;\r
- }\r
- }\r
- //We can still insert gaps if the selectionGroup\r
- //contains all the sequences\r
- sg.setEndRes(sg.getEndRes() + startres - lastres);\r
- fixedRight = alWidth + startres - lastres;\r
- }\r
- else\r
- {\r
- endEditing();\r
- return;\r
- }\r
- }\r
- }\r
-\r
- // drag to left\r
- else if (!insertGap)\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
-\r
- for (g = 0; g < groupSize; g++)\r
- {\r
- for (int j = startres; j < lastres; j++)\r
- {\r
- if (groupSeqs[g].getLength() <= j)\r
- {\r
- continue;\r
- }\r
-\r
- if (!jalview.util.Comparison.isGap(\r
- groupSeqs[g].getCharAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- endEditing();\r
- return;\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (insertGap)\r
- {\r
- // dragging to the right\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j < startres; j++)\r
- {\r
- insertChar(j, groupSeqs, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- groupSeqs,\r
- startres, startres - lastres,\r
- av.alignment,\r
- true);\r
- }\r
- }\r
- else\r
- {\r
- // dragging to the left\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j > startres; j--)\r
- {\r
- deleteChar(startres, groupSeqs, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- groupSeqs,\r
- startres, lastres - startres,\r
- av.alignment,\r
- true);\r
- }\r
-\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (insertGap)\r
- {\r
- // dragging to the right\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j < startres; j++)\r
- {\r
- insertChar(j, new SequenceI[]\r
- {seq}, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- new SequenceI[]\r
- {seq},\r
- lastres, startres - lastres,\r
- av.alignment,\r
- true);\r
- }\r
- }\r
- else\r
- {\r
- // dragging to the left\r
- if (fixedColumns && fixedRight != -1)\r
- {\r
- for (int j = lastres; j > startres; j--)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))\r
- {\r
- endEditing();\r
- break;\r
- }\r
- deleteChar(startres, new SequenceI[]\r
- {seq}, fixedRight);\r
- }\r
- }\r
- else\r
- {\r
- //could be a keyboard edit trying to delete none gaps\r
- int max = 0;\r
- for (int m = startres; m < lastres; m++)\r
- {\r
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))\r
- {\r
- break;\r
- }\r
- max++;\r
- }\r
-\r
- if (max > 0)\r
- {\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- new SequenceI[]\r
- {seq},\r
- startres, max,\r
- av.alignment,\r
- true);\r
- }\r
- }\r
- }\r
- }\r
-\r
- lastres = startres;\r
- seqCanvas.repaint();\r
- }\r
-\r
- void insertChar(int j, SequenceI[] seq, int fixedColumn)\r
- {\r
- int blankColumn = fixedColumn;\r
- for (int s = 0; s < seq.length; s++)\r
- {\r
- //Find the next gap before the end of the visible region boundary\r
- //If lastCol > j, theres a boundary after the gap insertion\r
-\r
- for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)\r
- {\r
- if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))\r
- {\r
- //Theres a space, so break and insert the gap\r
- break;\r
- }\r
- }\r
-\r
- if (blankColumn <= j)\r
- {\r
- blankColumn = fixedColumn;\r
- endEditing();\r
- return;\r
- }\r
- }\r
-\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- seq,\r
- blankColumn, 1, av.alignment, true);\r
-\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- seq,\r
- j, 1, av.alignment,\r
- true);\r
-\r
- }\r
-\r
- void deleteChar(int j, SequenceI[] seq, int fixedColumn)\r
- {\r
-\r
- editCommand.appendEdit(EditCommand.DELETE_GAP,\r
- seq,\r
- j, 1, av.alignment, true);\r
-\r
- editCommand.appendEdit(EditCommand.INSERT_GAP,\r
- seq,\r
- fixedColumn, 1, av.alignment, true);\r
- }\r
-\r
-//////////////////////////////////////////\r
-/////Everything below this is for defining the boundary of the rubberband\r
-//////////////////////////////////////////\r
- public void doMousePressedDefineMode(MouseEvent evt)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- scrollThread = null;\r
- }\r
-\r
- int res = findRes(evt);\r
- int seq = findSeq(evt);\r
- oldSeq = seq;\r
- startWrapBlock = wrappedBlock;\r
-\r
- if (seq == -1)\r
- {\r
- return;\r
- }\r
-\r
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
-\r
- if (sequence == null || res > sequence.getLength())\r
- {\r
- return;\r
- }\r
-\r
- stretchGroup = av.getSelectionGroup();\r
-\r
- if (stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup(sequence);\r
- if (stretchGroup != null && res > stretchGroup.getStartRes() &&\r
- res < stretchGroup.getEndRes())\r
- {\r
- av.setSelectionGroup(stretchGroup);\r
- }\r
- else\r
- {\r
- stretchGroup = null;\r
- }\r
- }\r
-\r
- else if (!stretchGroup.getSequences(null).contains(sequence)\r
- || stretchGroup.getStartRes() > res\r
- || stretchGroup.getEndRes() < res)\r
- {\r
- stretchGroup = null;\r
-\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);\r
-\r
- if (allGroups != null)\r
- {\r
- for (int i = 0; i < allGroups.length; i++)\r
- {\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- break;\r
- }\r
- }\r
- }\r
- av.setSelectionGroup(stretchGroup);\r
- }\r
-\r
- // DETECT RIGHT MOUSE BUTTON IN AWT\r
- if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
- InputEvent.BUTTON3_MASK)\r
- {\r
- SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,\r
- sequence.findPosition(res));\r
-\r
- Vector links = null;\r
- if (allFeatures != null)\r
- {\r
- for (int i = 0; i < allFeatures.length; i++)\r
- {\r
- if (allFeatures[i].links != null)\r
- {\r
- links = new Vector();\r
- for (int j = 0; j < allFeatures[i].links.size(); j++)\r
- {\r
- links.addElement(allFeatures[i].links.elementAt(j));\r
- }\r
- }\r
- }\r
- }\r
- APopupMenu popup = new APopupMenu(ap, null, links);\r
- this.add(popup);\r
- popup.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
- if (av.cursorMode)\r
- {\r
- seqCanvas.cursorX = findRes(evt);\r
- seqCanvas.cursorY = findSeq(evt);\r
- seqCanvas.repaint();\r
- return;\r
- }\r
-\r
- //Only if left mouse button do we want to change group sizes\r
-\r
- if (stretchGroup == null)\r
- {\r
- // define a new group here\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- sg.addSequence(sequence, false);\r
- av.setSelectionGroup(sg);\r
- stretchGroup = sg;\r
-\r
- if (av.getConservationSelected())\r
- {\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),\r
- "Background");\r
- }\r
- if (av.getAbovePIDThreshold())\r
- {\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),\r
- "Background");\r
- }\r
-\r
- }\r
- }\r
-\r
- public void doMouseReleasedDefineMode(MouseEvent evt)\r
- {\r
- if (stretchGroup == null)\r
- {\r
- return;\r
- }\r
-\r
- if (stretchGroup.cs != null)\r
- {\r
- if (stretchGroup.cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(\r
- stretchGroup.getSequences(av.hiddenRepSequences),\r
- stretchGroup.getWidth());\r
- }\r
-\r
- if (stretchGroup.cs instanceof Blosum62ColourScheme\r
- || stretchGroup.cs instanceof PIDColourScheme\r
- || stretchGroup.cs.conservationApplied()\r
- || stretchGroup.cs.getThreshold() > 0)\r
- {\r
- stretchGroup.recalcConservation();\r
- }\r
-\r
- if (stretchGroup.cs.conservationApplied())\r
- {\r
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,\r
- stretchGroup.getName());\r
- stretchGroup.recalcConservation();\r
- }\r
- else\r
- {\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
- stretchGroup.getName());\r
- }\r
- }\r
- changeEndRes = false;\r
- changeStartRes = false;\r
- stretchGroup = null;\r
- PaintRefresher.Refresh(ap, av.getSequenceSetId());\r
- ap.paintAlignment(true);\r
- }\r
-\r
- public void doMouseDraggedDefineMode(MouseEvent evt)\r
- {\r
- int res = findRes(evt);\r
- int y = findSeq(evt);\r
-\r
- if (wrappedBlock != startWrapBlock)\r
- {\r
- return;\r
- }\r
-\r
- if (stretchGroup == null)\r
- {\r
- return;\r
- }\r
-\r
- mouseDragging = true;\r
-\r
- if (y > av.alignment.getHeight())\r
- {\r
- y = av.alignment.getHeight() - 1;\r
- }\r
-\r
- if (res >= av.alignment.getWidth())\r
- {\r
- res = av.alignment.getWidth() - 1;\r
- }\r
-\r
- if (stretchGroup.getEndRes() == res)\r
- {\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
- }\r
- else if (stretchGroup.getStartRes() == res)\r
- {\r
- // Edit start res position of selected group\r
- changeStartRes = true;\r
- }\r
-\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- if (changeEndRes)\r
- {\r
- if (res > (stretchGroup.getStartRes() - 1))\r
- {\r
- stretchGroup.setEndRes(res);\r
- }\r
- }\r
- else if (changeStartRes)\r
- {\r
- if (res < (stretchGroup.getEndRes() + 1))\r
- {\r
- stretchGroup.setStartRes(res);\r
- }\r
- }\r
-\r
- int dragDirection = 0;\r
-\r
- if (y > oldSeq)\r
- {\r
- dragDirection = 1;\r
- }\r
- else if (y < oldSeq)\r
- {\r
- dragDirection = -1;\r
- }\r
-\r
- while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))\r
- {\r
- // This routine ensures we don't skip any sequences, as the\r
- // selection is quite slow.\r
- Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
-\r
- oldSeq += dragDirection;\r
-\r
- if (oldSeq < 0)\r
- {\r
- break;\r
- }\r
-\r
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
-\r
- if (stretchGroup.getSequences(null).contains(nextSeq))\r
- {\r
- stretchGroup.deleteSequence(seq, false);\r
- }\r
- else\r
- {\r
- if (seq != null)\r
- {\r
- stretchGroup.addSequence(seq, false);\r
- }\r
-\r
- stretchGroup.addSequence(nextSeq, false);\r
- }\r
- }\r
-\r
- if (oldSeq < 0)\r
- {\r
- oldSeq = -1;\r
- }\r
-\r
- if (res > av.endRes || res < av.startRes\r
- || y < av.startSeq || y > av.endSeq)\r
- {\r
- mouseExited(evt);\r
- }\r
-\r
- if (scrollThread != null)\r
- {\r
- scrollThread.setEvent(evt);\r
- }\r
-\r
- seqCanvas.repaint();\r
- }\r
-\r
- public void mouseEntered(MouseEvent e)\r
- {\r
- if (oldSeq < 0)\r
- {\r
- oldSeq = 0;\r
- }\r
-\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- scrollThread = null;\r
- }\r
- }\r
-\r
- public void mouseExited(MouseEvent e)\r
- {\r
- if (av.getWrapAlignment())\r
- {\r
- return;\r
- }\r
-\r
- if (mouseDragging && scrollThread == null)\r
- {\r
- scrollThread = new ScrollThread();\r
- }\r
- }\r
-\r
- void scrollCanvas(MouseEvent evt)\r
- {\r
- if (evt == null)\r
- {\r
- if (scrollThread != null)\r
- {\r
- scrollThread.running = false;\r
- scrollThread = null;\r
- }\r
- mouseDragging = false;\r
- }\r
- else\r
- {\r
- if (scrollThread == null)\r
- {\r
- scrollThread = new ScrollThread();\r
- }\r
-\r
- mouseDragging = true;\r
- scrollThread.setEvent(evt);\r
- }\r
-\r
- }\r
-\r
- // this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread\r
- extends Thread\r
- {\r
- MouseEvent evt;\r
- boolean running = false;\r
- public ScrollThread()\r
- {\r
- start();\r
- }\r
-\r
- public void setEvent(MouseEvent e)\r
- {\r
- evt = e;\r
- }\r
-\r
- public void stopScrolling()\r
- {\r
- running = false;\r
- }\r
-\r
- public void run()\r
- {\r
- running = true;\r
- while (running)\r
- {\r
-\r
- if (evt != null)\r
- {\r
-\r
- if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
- {\r
- running = ap.scrollUp(true);\r
- }\r
-\r
- if (mouseDragging && evt.getY() >= getSize().height &&\r
- av.alignment.getHeight() > av.getEndSeq())\r
- {\r
- running = ap.scrollUp(false);\r
- }\r
-\r
- if (mouseDragging && evt.getX() < 0)\r
- {\r
- running = ap.scrollRight(false);\r
- }\r
-\r
- else if (mouseDragging && evt.getX() >= getSize().width)\r
- {\r
- running = ap.scrollRight(true);\r
- }\r
- }\r
-\r
- try\r
- {\r
- Thread.sleep(75);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+
+public class SeqPanel
+ extends Panel implements MouseMotionListener, MouseListener, SequenceListener
+{
+
+ public SeqCanvas seqCanvas;
+ public AlignmentPanel ap;
+
+ protected int lastres;
+ protected int startseq;
+
+ protected AlignViewport av;
+
+ // if character is inserted or deleted, we will need to recalculate the conservation
+ boolean seqEditOccurred = false;
+
+ ScrollThread scrollThread = null;
+ boolean mouseDragging = false;
+ boolean editingSeqs = false;
+ boolean groupEditing = false;
+
+ int oldSeq = -1;
+ boolean changeEndSeq = false;
+ boolean changeStartSeq = false;
+ boolean changeEndRes = false;
+ boolean changeStartRes = false;
+ SequenceGroup stretchGroup = null;
+
+ StringBuffer keyboardNo1;
+ StringBuffer keyboardNo2;
+
+ boolean mouseWheelPressed = false;
+ Point lastMousePress;
+
+ EditCommand editCommand;
+
+ StructureSelectionManager ssm;
+
+
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)
+ {
+ this.av = avp;
+
+ seqCanvas = new SeqCanvas(avp);
+ setLayout(new BorderLayout());
+ add(seqCanvas);
+
+ ap = p;
+
+ seqCanvas.addMouseMotionListener(this);
+ seqCanvas.addMouseListener(this);
+ ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
+
+ seqCanvas.repaint();
+ }
+
+ void endEditing()
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
+ {
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
+ }
+
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
+ }
+
+ void setCursorRow()
+ {
+ seqCanvas.cursorY = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorColumn()
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorRowAndColumn()
+ {
+ if (keyboardNo2 == null)
+ {
+ keyboardNo2 = new StringBuffer();
+ }
+ else
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ seqCanvas.cursorY = getKeyboardNo2() - 1;
+ scrollToVisible();
+ }
+ }
+
+ void setCursorPosition()
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(
+ getKeyboardNo1() - 1
+ );
+ scrollToVisible();
+ }
+
+ void moveCursor(int dx, int dy)
+ {
+ seqCanvas.cursorX += dx;
+ seqCanvas.cursorY += dy;
+ if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ int original = seqCanvas.cursorX - dx;
+ int maxWidth = av.alignment.getWidth();
+
+ while (!av.colSel.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth
+ && seqCanvas.cursorX > 0)
+ {
+ seqCanvas.cursorX += dx;
+ }
+
+ if (seqCanvas.cursorX >= maxWidth
+ || !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ seqCanvas.cursorX = original;
+ }
+ }
+ scrollToVisible();
+ }
+
+ void scrollToVisible()
+ {
+ if (seqCanvas.cursorX < 0)
+ {
+ seqCanvas.cursorX = 0;
+ }
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ {
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ }
+
+ if (seqCanvas.cursorY < 0)
+ {
+ seqCanvas.cursorY = 0;
+ }
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ {
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ }
+
+ endEditing();
+ if (av.wrapAlignment)
+ {
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ }
+ else
+ {
+ while (seqCanvas.cursorY < av.startSeq)
+ {
+ ap.scrollUp(true);
+ }
+ while (seqCanvas.cursorY + 1 > av.endSeq)
+ {
+ ap.scrollUp(false);
+ }
+ while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+ {
+
+ if (!ap.scrollRight(false))
+ {
+ break;
+ }
+ }
+ while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
+ {
+ if (!ap.scrollRight(true))
+ {
+ break;
+ }
+ }
+ }
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
+
+ seqCanvas.repaint();
+ }
+
+ void setSelectionAreaAtCursor(boolean topLeft)
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ if (av.getSelectionGroup() != null)
+ {
+ SequenceGroup sg = av.selectionGroup;
+ //Find the top and bottom of this group
+ int min = av.alignment.getHeight(), max = 0;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ if (index > max)
+ {
+ max = index;
+ }
+ if (index < min)
+ {
+ min = index;
+ }
+ }
+
+ max++;
+
+ if (topLeft)
+ {
+ sg.setStartRes(seqCanvas.cursorX);
+ if (sg.getEndRes() < seqCanvas.cursorX)
+ {
+ sg.setEndRes(seqCanvas.cursorX);
+ }
+
+ min = seqCanvas.cursorY;
+ }
+ else
+ {
+ sg.setEndRes(seqCanvas.cursorX);
+ if (sg.getStartRes() > seqCanvas.cursorX)
+ {
+ sg.setStartRes(seqCanvas.cursorX);
+ }
+
+ max = seqCanvas.cursorY + 1;
+ }
+
+ if (min > max)
+ {
+ // Only the user can do this
+ av.setSelectionGroup(null);
+ }
+ else
+ {
+ // Now add any sequences between min and max
+ sg.getSequences(null).removeAllElements();
+ for (int i = min; i < max; i++)
+ {
+ sg.addSequence(av.alignment.getSequenceAt(i), false);
+ }
+ }
+ }
+
+ if (av.getSelectionGroup() == null)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(seqCanvas.cursorX);
+ sg.setEndRes(seqCanvas.cursorX);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ }
+
+ ap.paintAlignment(false);
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX + getKeyboardNo1();
+ editSequence(false, seqCanvas.cursorX);
+ endEditing();
+ }
+
+ void numberPressed(char value)
+ {
+ if (keyboardNo1 == null)
+ {
+ keyboardNo1 = new StringBuffer();
+ }
+
+ if (keyboardNo2 != null)
+ {
+ keyboardNo2.append(value);
+ }
+ else
+ {
+ keyboardNo1.append(value);
+ }
+ }
+
+ int getKeyboardNo1()
+ {
+ if (keyboardNo1 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ }
+
+ int getKeyboardNo2()
+ {
+ if (keyboardNo2 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ }
+
+
+ void setStatusMessage(SequenceI sequence, int res, int seq)
+ {
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+ sequence.getName());
+
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+ "");
+ if (obj != null)
+ {
+ text.append(" Nucleotide: ");
+ }
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ if (obj != null)
+ {
+ text.append(" Residue: ");
+ }
+ }
+
+ if (obj != null)
+ {
+
+ if (obj != "")
+ {
+ text.append(obj + " (" + sequence.findPosition(res) +
+ ")");
+ }
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ //For now, ignore the mouseWheel font resizing on Macs
+ //As the Button2_mask always seems to be true
+ if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
+ InputEvent.BUTTON2_MASK && !av.MAC)
+ {
+ mouseWheelPressed = true;
+ return;
+ }
+
+ if (evt.isShiftDown()
+ || evt.isControlDown()
+ || evt.isAltDown())
+ {
+ if (evt.isControlDown() || evt.isAltDown())
+ {
+ groupEditing = true;
+ }
+ editingSeqs = true;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
+
+ if ( (seq < av.getAlignment().getHeight()) &&
+ (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ {
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ if (evt.getClickCount() > 1)
+ {
+ if (av.getSelectionGroup().getSize() == 1
+ && av.getSelectionGroup().getEndRes()
+ - av.getSelectionGroup().getStartRes() < 2)
+ {
+ av.setSelectionGroup(null);
+ }
+
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence,
+ sequence.findPosition(findRes(evt))
+ );
+
+ if (features != null && features.length > 0)
+ {
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequence,
+ features[0].getBegin(),
+ features[0].getEnd());
+ seqCanvas.highlightSearchResults(highlight);
+ }
+ if (features != null && features.length > 0)
+ {
+ seqCanvas.getFeatureRenderer().amendFeatures(
+ new SequenceI[]
+ {sequence}, features, false, ap);
+
+ seqCanvas.highlightSearchResults(null);
+ }
+ }
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+ mouseWheelPressed = false;
+ ap.paintAlignment(true);
+
+ if (!editingSeqs)
+ {
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ endEditing();
+
+ }
+
+ int startWrapBlock = -1;
+ int wrappedBlock = -1;
+ int findRes(MouseEvent evt)
+ {
+ int res = 0;
+ int x = evt.getX();
+
+ if (av.wrapAlignment)
+ {
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ int y = evt.getY();
+ y -= hgap;
+ x -= seqCanvas.LABEL_WEST;
+
+ int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width);
+ if (cwidth < 1)
+ {
+ return 0;
+ }
+
+ wrappedBlock = y / cHeight;
+ wrappedBlock += av.getStartRes() / cwidth;
+
+ res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+ }
+ else
+ {
+ res = (x / av.getCharWidth()) + av.getStartRes();
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
+
+ return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+
+ int seq = 0;
+ int y = evt.getY();
+
+ if (av.wrapAlignment)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ y -= hgap;
+
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() - 1);
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ }
+ else
+ {
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() - 1);
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ }
+
+ return seq;
+ }
+
+
+
+ public void doMousePressed(MouseEvent evt)
+ {
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < av.getAlignment().getHeight() &&
+ res < av.getAlignment().getSequenceAt(seq).getLength())
+ {
+ //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
+ // Find the residue's position in the sequence (res is the position
+ // in the alignment
+
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+
+ String lastMessage;
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)
+ {
+ String tmp = sequence.hashCode()+index+"";
+ if (lastMessage == null || !lastMessage.equals(tmp))
+ ssm.mouseOverSequence(sequence, index, pos);
+
+ lastMessage = tmp;
+ }
+
+
+ public void highlightSequence(SearchResults results)
+ {
+ seqCanvas.highlightSearchResults(results);
+ }
+
+ public void updateColours(SequenceI seq, int index)
+ {
+ System.out.println("update the seqPanel colours");
+ //repaint();
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+
+ if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+ {
+ if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ return;
+ }
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ if (res > sequence.getLength())
+ {
+ if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ return;
+ }
+
+ int respos = sequence.findPosition(res);
+ if (ssm != null)
+ mouseOverSequence(sequence, res, respos);
+
+
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+ sequence.getName());
+
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+ "");
+ if (obj != null)
+ {
+ text.append(" Nucleotide: ");
+ }
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ if (obj != null)
+ {
+ text.append(" Residue: ");
+ }
+ }
+
+ if (obj != null)
+ {
+ if (obj != "")
+ {
+ text.append(obj + " (" + respos + ")");
+ }
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+
+ StringBuffer tooltipText = new StringBuffer();
+ SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ if (groups != null)
+ {
+ for (int g = 0; g < groups.length; g++)
+ {
+ if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ {
+ if (!groups[g].getName().startsWith("JTreeGroup") &&
+ !groups[g].getName().startsWith("JGroup"))
+ {
+ tooltipText.append(groups[g].getName() + " ");
+ }
+ if (groups[g].getDescription() != null)
+ {
+ tooltipText.append(groups[g].getDescription());
+ }
+ tooltipText.append("\n");
+ }
+ }
+ }
+
+ // use aa to see if the mouse pointer is on a
+ SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
+
+ int index = 0;
+ while (index < allFeatures.length)
+ {
+ SequenceFeature sf = allFeatures[index];
+
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+
+ if (sf.getDescription() != null)
+ {
+ tooltipText.append(" " + sf.getDescription());
+ }
+
+ if (sf.getValue("status") != null)
+ {
+ String status = sf.getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText.append(" (" + sf.getValue("status") + ")");
+ }
+ }
+ tooltipText.append("\n");
+
+ index++;
+ }
+
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
+ }
+ else
+ {
+ tooltip.setTip(tooltipText.toString());
+ }
+ }
+
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ Vector tmp = new Vector();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (av.featuresDisplayed == null
+ || !av.featuresDisplayed.containsKey(features[i].getType()))
+ {
+ continue;
+ }
+
+
+
+ if (features[i].featureGroup != null
+ && seqCanvas.fr.featureGroups!=null
+ && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)
+ && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())
+ continue;
+
+
+ if ( (features[i].getBegin() <= res) &&
+ (features[i].getEnd() >= res))
+ {
+ tmp.addElement(features[i]);
+ }
+ }
+ }
+
+ features = new SequenceFeature[tmp.size()];
+ tmp.copyInto(features);
+
+ return features;
+ }
+
+
+ Tooltip tooltip;
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (mouseWheelPressed)
+ {
+ int oldWidth = av.charWidth;
+
+ //Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.y)
+ > Math.abs(evt.getX() - lastMousePress.x))
+ {
+ int fontSize = av.font.getSize();
+
+ if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ {
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.y)
+ {
+ fontSize++;
+ }
+
+ if (fontSize < 1)
+ {
+ fontSize = 1;
+ }
+
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.charWidth = oldWidth;
+ }
+ else
+ {
+ if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ {
+ av.charWidth--;
+ }
+ else if (evt.getX() > lastMousePress.x)
+ {
+ av.charWidth++;
+ }
+
+ if (av.charWidth < 1)
+ {
+ av.charWidth = 1;
+ }
+ }
+
+ ap.fontChanged();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+ lastMousePress = evt.getPoint();
+
+ ap.paintAlignment(false);
+ ap.annotationPanel.image = null;
+ return;
+ }
+
+ if (!editingSeqs)
+ {
+ doMouseDraggedDefineMode(evt);
+ return;
+ }
+
+ int res = findRes(evt);
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if ( (lastres == -1) || (lastres == res))
+ {
+ return;
+ }
+
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+ {
+ // dragLeft, delete gap
+ editSequence(false, res);
+ }
+ else
+ {
+ editSequence(true, res);
+ }
+
+ mouseDragging = true;
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ synchronized void editSequence(boolean insertGap, int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+ if (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(seq))
+ {
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuffer message = new StringBuffer();
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit Group");
+ }
+ }
+ else
+ {
+ message.append("Edit sequence: " + seq.getName());
+ String label = seq.getName();
+ if (label.length() > 10)
+ {
+ label = label.substring(0, 10);
+ }
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit " + label);
+ }
+ }
+
+ if (insertGap)
+ {
+ message.append(" insert ");
+ }
+ else
+ {
+ message.append(" delete ");
+ }
+
+ message.append(Math.abs(startres - lastres) + " gaps.");
+ ap.alignFrame.statusBar.setText(message.toString());
+
+ //Are we editing within a selection group?
+ if (groupEditing
+ || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+ {
+ fixedColumns = true;
+
+ //sg might be null as the user may only see 1 sequence,
+ //but the sequence represents a group
+ if (sg == null)
+ {
+ if (av.hiddenRepSequences == null
+ || !av.hiddenRepSequences.containsKey(seq))
+ {
+ endEditing();
+ return;
+ }
+
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ }
+
+ fixedLeft = sg.getStartRes();
+ fixedRight = sg.getEndRes();
+
+ if ( (startres < fixedLeft && lastres >= fixedLeft)
+ || (startres >= fixedLeft && lastres < fixedLeft)
+ || (startres > fixedRight && lastres <= fixedRight)
+ || (startres <= fixedRight && lastres > fixedRight))
+ {
+ endEditing();
+ return;
+ }
+
+ if (fixedLeft > startres)
+ {
+ fixedRight = fixedLeft - 1;
+ fixedLeft = 0;
+ }
+ else if (fixedRight < startres)
+ {
+ fixedLeft = fixedRight;
+ fixedRight = -1;
+ }
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ fixedColumns = true;
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+
+ if ( (insertGap && startres > y1 && lastres < y1)
+ || (!insertGap && startres < y2 && lastres > y2))
+ {
+ endEditing();
+ return;
+ }
+
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ //Selection spans a hidden region
+ if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+ {
+ if (startres >= y2)
+ {
+ fixedLeft = y2;
+ }
+ else
+ {
+ fixedRight = y2 - 1;
+ }
+ }
+ }
+
+ if (groupEditing)
+ {
+ Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+ int g, groupSize = vseqs.size();
+ SequenceI[] groupSeqs = new SequenceI[groupSize];
+ for (g = 0; g < groupSeqs.length; g++)
+ {
+ groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+ }
+
+ // drag to right
+ if (insertGap)
+ {
+ //If the user has selected the whole sequence, and is dragging to
+ // the right, we can still extend the alignment and selectionGroup
+ if (sg.getStartRes() == 0
+ && sg.getEndRes() == fixedRight
+ && sg.getEndRes() == av.alignment.getWidth() - 1
+ )
+ {
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ fixedRight = sg.getEndRes();
+ }
+
+ // Is it valid with fixed columns??
+ // Find the next gap before the end
+ // of the visible region boundary
+ boolean blank = false;
+ for (fixedRight = fixedRight;
+ fixedRight > lastres;
+ fixedRight--)
+ {
+ blank = true;
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!jalview.util.Comparison.isGap(
+ groupSeqs[g].getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ {
+ break;
+ }
+ }
+
+ if (!blank)
+ {
+ if (sg.getSize() == av.alignment.getHeight())
+ {
+ if ( (av.hasHiddenColumns
+ &&
+ startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
+ {
+ endEditing();
+ return;
+ }
+
+ int alWidth = av.alignment.getWidth();
+ if (av.hasHiddenRows)
+ {
+ int hwidth = av.alignment.getHiddenSequences().getWidth();
+ if (hwidth > alWidth)
+ {
+ alWidth = hwidth;
+ }
+ }
+ //We can still insert gaps if the selectionGroup
+ //contains all the sequences
+ sg.setEndRes(sg.getEndRes() + startres - lastres);
+ fixedRight = alWidth + startres - lastres;
+ }
+ else
+ {
+ endEditing();
+ return;
+ }
+ }
+ }
+
+ // drag to left
+ else if (!insertGap)
+ {
+ /// Are we able to delete?
+ // ie are all columns blank?
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = startres; j < lastres; j++)
+ {
+ if (groupSeqs[g].getLength() <= j)
+ {
+ continue;
+ }
+
+ if (!jalview.util.Comparison.isGap(
+ groupSeqs[g].getCharAt(j)))
+ {
+ // Not a gap, block edit not valid
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
+
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ groupSeqs,
+ startres, startres - lastres,
+ av.alignment,
+ true);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ groupSeqs,
+ startres, lastres - startres,
+ av.alignment,
+ true);
+ }
+
+ }
+ }
+ else /////Editing a single sequence///////////
+ {
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[]
+ {seq}, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ new SequenceI[]
+ {seq},
+ lastres, startres - lastres,
+ av.alignment,
+ true);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[]
+ {seq}, fixedRight);
+ }
+ }
+ else
+ {
+ //could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ new SequenceI[]
+ {seq},
+ startres, max,
+ av.alignment,
+ true);
+ }
+ }
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
+
+ void insertChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+ int blankColumn = fixedColumn;
+ for (int s = 0; s < seq.length; s++)
+ {
+ //Find the next gap before the end of the visible region boundary
+ //If lastCol > j, theres a boundary after the gap insertion
+
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ {
+ //Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
+ }
+
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ seq,
+ blankColumn, 1, av.alignment, true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ seq,
+ j, 1, av.alignment,
+ true);
+
+ }
+
+ void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ seq,
+ j, 1, av.alignment, true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ seq,
+ fixedColumn, 1, av.alignment, true);
+ }
+
+//////////////////////////////////////////
+/////Everything below this is for defining the boundary of the rubberband
+//////////////////////////////////////////
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ oldSeq = seq;
+ startWrapBlock = wrappedBlock;
+
+ if (seq == -1)
+ {
+ return;
+ }
+
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+ if (sequence == null || res > sequence.getLength())
+ {
+ return;
+ }
+
+ stretchGroup = av.getSelectionGroup();
+
+ if (stretchGroup == null)
+ {
+ stretchGroup = av.alignment.findGroup(sequence);
+ if (stretchGroup != null && res > stretchGroup.getStartRes() &&
+ res < stretchGroup.getEndRes())
+ {
+ av.setSelectionGroup(stretchGroup);
+ }
+ else
+ {
+ stretchGroup = null;
+ }
+ }
+
+ else if (!stretchGroup.getSequences(null).contains(sequence)
+ || stretchGroup.getStartRes() > res
+ || stretchGroup.getEndRes() < res)
+ {
+ stretchGroup = null;
+
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+ if (allGroups != null)
+ {
+ for (int i = 0; i < allGroups.length; i++)
+ {
+ if (allGroups[i].getStartRes() <= res &&
+ allGroups[i].getEndRes() >= res)
+ {
+ stretchGroup = allGroups[i];
+ break;
+ }
+ }
+ }
+ av.setSelectionGroup(stretchGroup);
+ }
+
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+ InputEvent.BUTTON3_MASK)
+ {
+ SequenceFeature [] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
+
+ Vector links = null;
+ if (allFeatures != null)
+ {
+ for (int i = 0; i < allFeatures.length; i++)
+ {
+ if (allFeatures[i].links != null)
+ {
+ links = new Vector();
+ for (int j = 0; j < allFeatures[i].links.size(); j++)
+ {
+ links.addElement(allFeatures[i].links.elementAt(j));
+ }
+ }
+ }
+ }
+ APopupMenu popup = new APopupMenu(ap, null, links);
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ //Only if left mouse button do we want to change group sizes
+
+ if (stretchGroup == null)
+ {
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+
+ }
+ }
+
+ public void doMouseReleasedDefineMode(MouseEvent evt)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ if (stretchGroup.cs != null)
+ {
+ if (stretchGroup.cs instanceof ClustalxColourScheme)
+ {
+ ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+ stretchGroup.getSequences(av.hiddenRepSequences),
+ stretchGroup.getWidth());
+ }
+
+ if (stretchGroup.cs instanceof Blosum62ColourScheme
+ || stretchGroup.cs instanceof PIDColourScheme
+ || stretchGroup.cs.conservationApplied()
+ || stretchGroup.cs.getThreshold() > 0)
+ {
+ stretchGroup.recalcConservation();
+ }
+
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ stretchGroup.recalcConservation();
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ ap.paintAlignment(true);
+ }
+
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int y = findSeq(evt);
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ mouseDragging = true;
+
+ if (y > av.alignment.getHeight())
+ {
+ y = av.alignment.getHeight() - 1;
+ }
+
+ if (res >= av.alignment.getWidth())
+ {
+ res = av.alignment.getWidth() - 1;
+ }
+
+ if (stretchGroup.getEndRes() == res)
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if (stretchGroup.getStartRes() == res)
+ {
+ // Edit start res position of selected group
+ changeStartRes = true;
+ }
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if (changeEndRes)
+ {
+ if (res > (stretchGroup.getStartRes() - 1))
+ {
+ stretchGroup.setEndRes(res);
+ }
+ }
+ else if (changeStartRes)
+ {
+ if (res < (stretchGroup.getEndRes() + 1))
+ {
+ stretchGroup.setStartRes(res);
+ }
+ }
+
+ int dragDirection = 0;
+
+ if (y > oldSeq)
+ {
+ dragDirection = 1;
+ }
+ else if (y < oldSeq)
+ {
+ dragDirection = -1;
+ }
+
+ while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ {
+ // This routine ensures we don't skip any sequences, as the
+ // selection is quite slow.
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ oldSeq += dragDirection;
+
+ if (oldSeq < 0)
+ {
+ break;
+ }
+
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ if (stretchGroup.getSequences(null).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ if (res > av.endRes || res < av.startRes
+ || y < av.startSeq || y > av.endSeq)
+ {
+ mouseExited(evt);
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ {
+ oldSeq = 0;
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ void scrollCanvas(MouseEvent evt)
+ {
+ if (evt == null)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ mouseDragging = false;
+ }
+ else
+ {
+ if (scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+
+ mouseDragging = true;
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread
+ extends Thread
+ {
+ MouseEvent evt;
+ boolean running = false;
+ public ScrollThread()
+ {
+ start();
+ }
+
+ public void setEvent(MouseEvent e)
+ {
+ evt = e;
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+ while (running)
+ {
+
+ if (evt != null)
+ {
+
+ if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+ {
+ running = ap.scrollUp(true);
+ }
+
+ if (mouseDragging && evt.getY() >= getSize().height &&
+ av.alignment.getHeight() > av.getEndSeq())
+ {
+ running = ap.scrollUp(false);
+ }
+
+ if (mouseDragging && evt.getX() < 0)
+ {
+ running = ap.scrollRight(false);
+ }
+
+ else if (mouseDragging && evt.getX() >= getSize().width)
+ {
+ running = ap.scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(75);
+ }
+ catch (Exception ex)
+ {}
+ }
+ }
+ }
+
+}
showTranslation.setVisible( nucleotide );
conservationMenuItem.setEnabled( !nucleotide );
modifyConservation.setEnabled( !nucleotide );
-
+
//Remember AlignFrame always starts as protein
if(!nucleotide)
{
calculateMenu.remove(calculateMenu.getItemCount()-2);
}
+ setShowProductsEnabled();
}
+
+
/**
* Need to call this method when tabs are selected for multiple views,
* or when loading from Jalview2XML.java
public void actionPerformed(ActionEvent e)
{
- new jalview.io.DBRefFetcher(
+ new jalview.ws.DBRefFetcher(
alignPanel.av.getSequenceSelection(),
alignPanel.alignFrame).fetchDBRefs(false);
}
vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
}
}*/
+ /**
+ * prototype of an automatically enabled/disabled analysis function
+ *
+ */
+ protected void setShowProductsEnabled()
+ {
+ SequenceI [] selection = viewport.getSequenceSelection();
+ if (canShowProducts(selection, viewport.getSelectionGroup()!=null, viewport.getAlignment().getDataset()))
+ {
+ showProducts.setEnabled(true);
+
+ } else {
+ showProducts.setEnabled(false);
+ }
+ }
+ /**
+ * search selection for sequence xRef products and build the
+ * show products menu.
+ * @param selection
+ * @param dataset
+ * @return true if showProducts menu should be enabled.
+ */
+ public boolean canShowProducts(SequenceI[] selection, boolean isRegionSelection, Alignment dataset)
+ {
+ boolean showp=false;
+ try {
+ showProducts.removeAll();
+ final boolean dna = viewport.getAlignment().isNucleotide();
+ String[] ptypes = CrossRef.findSequenceXrefTypes(dna, selection, dataset);
+ //Object[] prods = CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), selection, dataset, true);
+ final SequenceI[] sel = selection;
+ for (int t=0; ptypes!=null && t<ptypes.length; t++)
+ {
+ showp=true;
+ final boolean isRegSel = isRegionSelection;
+ final AlignFrame af = this;
+ final String source = ptypes[t];
+ JMenuItem xtype = new JMenuItem(ptypes[t]);
+ xtype.addActionListener(new ActionListener() {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ af.showProductsFor(sel, isRegSel, dna, source);
+ }
+
+ });
+ showProducts.add(xtype);
+ }
+ showProducts.setVisible(showp);
+ showProducts.setEnabled(showp);
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
+ return false;
+ }
+ return showp;
+ }
+protected void showProductsFor(SequenceI[] sel, boolean isRegSel, boolean dna, String source)
+ {
+ Alignment ds = getViewport().alignment.getDataset();
+ Alignment prods = CrossRef.findXrefSequences(sel, dna, source, ds);
+ if (prods!=null)
+ {
+ SequenceI[] sprods = new SequenceI[prods.getHeight()];
+ for (int s=0; s<sprods.length;s++)
+ {
+ sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
+ if (!ds.getSequences().contains(sprods[s].getDatasetSequence()))
+ ds.addSequence(sprods[s].getDatasetSequence());
+ }
+ Alignment al = new Alignment(sprods);
+ AlignedCodonFrame[] cf = prods.getCodonFrames();
+ for (int s=0; cf!=null && s<cf.length; s++)
+ {
+ al.addCodonFrame(cf[s]);
+ cf[s] = null;
+ }
+ al.setDataset(ds);
+ AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ String newtitle =""+((dna) ? "Proteins " : "Nucleotides ") + " for "+((isRegSel) ? "selected region of " : "")
+ + getTitle();
+ Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ } else {
+ System.err.println("No Sequences generated for xRef type "+source);
+ }
+ }
+
+public boolean canShowTranslationProducts(SequenceI[] selection, AlignmentI alignment)
+{
+ // old way
+ try {
+ return (jalview.analysis.Dna.canTranslate(selection, viewport.getViewAsVisibleContigs(true)));
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn("canTranslate threw an exception - please report to help@jalview.org",e);
+ return false;
+ }
+}
+public void showProducts_actionPerformed(ActionEvent e)
+{
+ ///////////////////////////////
+ // Collect Data to be translated/transferred
+
+ SequenceI [] selection = viewport.getSequenceSelection();
+ AlignmentI al = null;
+ try {
+ al = jalview.analysis.Dna.CdnaTranslate(selection, viewport.getViewAsVisibleContigs(true),
+ viewport.getGapCharacter(), viewport.getAlignment().getDataset());
+ } catch (Exception ex) {
+ al = null;
+ jalview.bin.Cache.log.debug("Exception during translation.",ex);
+ }
+ if (al==null)
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
+ "Translation Failed",
+ JOptionPane.WARNING_MESSAGE);
+ } else {
+ AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+ DEFAULT_WIDTH,
+ DEFAULT_HEIGHT);
+ }
+ }
public void showTranslation_actionPerformed(ActionEvent e)
{
try {
al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
- viewport.alignment.getWidth());
+ viewport.alignment.getWidth(), viewport.getAlignment().getDataset());
} catch (Exception ex) {
al = null;
jalview.bin.Cache.log.debug("Exception during translation.",ex);
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.ws.EBIFetchClient;
import org.jmol.api.*;
import org.jmol.adapter.smarter.SmarterJmolAdapter;
progressBar.setVisible(true);\r
progressBar.setIndeterminate(true);\r
\r
- dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();\r
+ dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
\r
appendLocalSources();\r
\r
{\r
if (dasSources == null)\r
{\r
- dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();\r
+ dasSources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
appendLocalSources();\r
}\r
\r
extends JPanel
{
DasSourceBrowser dassourceBrowser;
- jalview.io.DasSequenceFeatureFetcher dasFeatureFetcher;
+ jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
JPanel settingsPane = new JPanel();
JPanel dasSettingsPane = new JPanel();
}
dasFeatureFetcher =
- new jalview.io.DasSequenceFeatureFetcher(
+ new jalview.ws.DasSequenceFeatureFetcher(
dataset,
this,
selectedSources);
-/*\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.gui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import MCview.*;\r
-import jalview.analysis.*;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PopupMenu\r
- extends JPopupMenu\r
-{\r
- JMenu groupMenu = new JMenu();\r
- JMenuItem groupName = new JMenuItem();\r
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new\r
- JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
- AlignmentPanel ap;\r
- JMenu sequenceMenu = new JMenu();\r
- JMenuItem sequenceName = new JMenuItem();\r
- Sequence sequence;\r
- JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem outline = new JMenuItem();\r
- JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
- JMenu colourMenu = new JMenu();\r
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
- JMenu editMenu = new JMenu();\r
- JMenuItem cut = new JMenuItem();\r
- JMenuItem copy = new JMenuItem();\r
- JMenuItem upperCase = new JMenuItem();\r
- JMenuItem lowerCase = new JMenuItem();\r
- JMenuItem toggle = new JMenuItem();\r
- JMenu pdbMenu = new JMenu();\r
- JMenuItem pdbFromFile = new JMenuItem();\r
- JMenuItem enterPDB = new JMenuItem();\r
- JMenuItem discoverPDB = new JMenuItem();\r
- JMenu outputMenu = new JMenu();\r
- JMenuItem sequenceFeature = new JMenuItem();\r
- JMenuItem textColour = new JMenuItem();\r
- JMenu jMenu1 = new JMenu();\r
- JMenu structureMenu = new JMenu();\r
- JMenu viewStructureMenu = new JMenu();\r
- // JMenu colStructureMenu = new JMenu();\r
- JMenuItem editSequence = new JMenuItem();\r
- // JMenuItem annotationMenuItem = new JMenuItem();\r
-\r
- /**\r
- * Creates a new PopupMenu object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- */\r
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
- {\r
- ///////////////////////////////////////////////////////////\r
- // If this is activated from the sequence panel, the user may want to\r
- // edit or annotate a particular residue. Therefore display the residue menu\r
- //\r
- // If from the IDPanel, we must display the sequence menu\r
- //////////////////////////////////////////////////////////\r
- this.ap = ap;\r
- sequence = seq;\r
-\r
- ButtonGroup colours = new ButtonGroup();\r
- colours.add(noColourmenuItem);\r
- colours.add(clustalColour);\r
- colours.add(zappoColour);\r
- colours.add(taylorColour);\r
- colours.add(hydrophobicityColour);\r
- colours.add(helixColour);\r
- colours.add(strandColour);\r
- colours.add(turnColour);\r
- colours.add(buriedColour);\r
- colours.add(abovePIDColour);\r
- colours.add(userDefinedColour);\r
- colours.add(PIDColour);\r
- colours.add(BLOSUM62Colour);\r
-\r
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
- {\r
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
- i]);\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputMenu.add(item);\r
- }\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- if (seq != null)\r
- {\r
- sequenceMenu.setText(sequence.getName());\r
-\r
- JMenuItem menuItem;\r
- if (seq.getDatasetSequence().getPDBId() != null\r
- && seq.getDatasetSequence().getPDBId().size()>0)\r
- {\r
- java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
- elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- final PDBEntry pdb = (PDBEntry) e.nextElement();\r
-\r
- menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- Vector seqs = new Vector();\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
- {\r
- Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
- if(pdbs==null)\r
- continue;\r
-\r
- for(int p=0; p<pdbs.size(); p++)\r
- {\r
- PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
- if(p1.getId().equals(pdb.getId()))\r
- {\r
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
- seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
-\r
- continue;\r
- }\r
- }\r
- }\r
-\r
- SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
- seqs.toArray(seqs2);\r
-\r
- new AppJmol(pdb, seqs2, null, ap);\r
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
- }\r
- });\r
- viewStructureMenu.add(menuItem);\r
-\r
- /* menuItem = new JMenuItem();\r
- menuItem.setText(pdb.getId());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- colourByStructure(pdb.getId());\r
- }\r
- });\r
- colStructureMenu.add(menuItem);*/\r
- }\r
- }\r
- else\r
- {\r
- structureMenu.remove(viewStructureMenu);\r
- // structureMenu.remove(colStructureMenu);\r
- }\r
-\r
- menuItem = new JMenuItem("Hide Sequences");\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(false);\r
- }\r
- });\r
- add(menuItem);\r
-\r
- if (ap.av.getSelectionGroup() != null\r
- && ap.av.getSelectionGroup().getSize() > 1)\r
- {\r
- menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
- menuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hideSequences(true);\r
- }\r
- });\r
- sequenceMenu.add(menuItem);\r
- }\r
-\r
- if (ap.av.hasHiddenRows)\r
- {\r
- final int index = ap.av.alignment.findIndex(seq);\r
-\r
- if (ap.av.adjustForHiddenSeqs(index) -\r
- ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
- {\r
- menuItem = new JMenuItem("Reveal Sequences");\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showSequence(index);\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
- add(menuItem);\r
- }\r
-\r
- menuItem = new JMenuItem("Reveal All");\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ap.av.showAllHiddenSeqs();\r
- if (ap.overviewPanel != null)\r
- {\r
- ap.overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- });\r
-\r
- add(menuItem);\r
- }\r
-\r
- }\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- groupName.setText(sg.getName());\r
-\r
- if (sg.cs instanceof ZappoColourScheme)\r
- {\r
- zappoColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TaylorColourScheme)\r
- {\r
- taylorColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof PIDColourScheme)\r
- {\r
- PIDColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof Blosum62ColourScheme)\r
- {\r
- BLOSUM62Colour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof UserColourScheme)\r
- {\r
- userDefinedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HydrophobicColourScheme)\r
- {\r
- hydrophobicityColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof HelixColourScheme)\r
- {\r
- helixColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof StrandColourScheme)\r
- {\r
- strandColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof TurnColourScheme)\r
- {\r
- turnColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof BuriedColourScheme)\r
- {\r
- buriedColour.setSelected(true);\r
- }\r
- else if (sg.cs instanceof ClustalxColourScheme)\r
- {\r
- clustalColour.setSelected(true);\r
- }\r
- else\r
- {\r
- noColourmenuItem.setSelected(true);\r
- }\r
-\r
- if (sg.cs != null && sg.cs.conservationApplied())\r
- {\r
- conservationMenuItem.setSelected(true);\r
- }\r
-\r
- showText.setSelected(sg.getDisplayText());\r
- showColourText.setSelected(sg.getColourText());\r
- showBoxes.setSelected(sg.getDisplayBoxes());\r
- }\r
- else\r
- {\r
- groupMenu.setVisible(false);\r
- editMenu.setVisible(false);\r
- }\r
-\r
- if (!ap.av.alignment.getGroups().contains(sg))\r
- {\r
- unGroupMenuItem.setVisible(false);\r
- }\r
-\r
- if (seq == null)\r
- {\r
- sequenceMenu.setVisible(false);\r
- structureMenu.setVisible(false);\r
- }\r
-\r
- if (links != null && links.size() > 0)\r
- {\r
- JMenu linkMenu = new JMenu("Link");\r
- JMenuItem item;\r
- for (int i = 0; i < links.size(); i++)\r
- {\r
- String link = links.elementAt(i).toString();\r
- final String label = link.substring(0, link.indexOf("|"));\r
- item = new JMenuItem(label);\r
- final String url;\r
-\r
- if (link.indexOf("$SEQUENCE_ID$") > -1)\r
- {\r
- String id = seq.getName();\r
- if (id.indexOf("|") > -1)\r
- {\r
- id = id.substring(id.lastIndexOf("|") + 1);\r
- }\r
-\r
- url = link.substring(link.indexOf("|") + 1,\r
- link.indexOf("$SEQUENCE_ID$"))\r
- + id +\r
- link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
- }\r
- else\r
- {\r
- url = link.substring(link.lastIndexOf("|") + 1);\r
- }\r
-\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showLink(url);\r
- }\r
- });\r
-\r
- linkMenu.add(item);\r
- }\r
- if (sequence != null)\r
- {\r
- sequenceMenu.add(linkMenu);\r
- }\r
- else\r
- {\r
- add(linkMenu);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws Exception DOCUMENT ME!\r
- */\r
- private void jbInit()\r
- throws Exception\r
- {\r
- groupMenu.setText("Group");\r
- groupMenu.setText("Selection");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- groupName_actionPerformed();\r
- }\r
- });\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit Name/Description");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceName_actionPerformed();\r
- }\r
- });\r
- PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- outline.setText("Border colour");\r
- outline.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outline_actionPerformed();\r
- }\r
- });\r
- nucleotideMenuItem.setText("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed();\r
- }\r
- });\r
- colourMenu.setText("Group Colour");\r
- showBoxes.setText("Boxes");\r
- showBoxes.setState(true);\r
- showBoxes.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showBoxes_actionPerformed();\r
- }\r
- });\r
- showText.setText("Text");\r
- showText.setState(true);\r
- showText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showText_actionPerformed();\r
- }\r
- });\r
- showColourText.setText("Colour Text");\r
- showColourText.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- showColourText_actionPerformed();\r
- }\r
- });\r
- editMenu.setText("Edit");\r
- cut.setText("Cut");\r
- cut.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cut_actionPerformed();\r
- }\r
- });\r
- upperCase.setText("To Upper Case");\r
- upperCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- copy.setText("Copy");\r
- copy.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copy_actionPerformed();\r
- }\r
- });\r
- lowerCase.setText("To Lower Case");\r
- lowerCase.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- toggle.setText("Toggle Case");\r
- toggle.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e);\r
- }\r
- });\r
- pdbMenu.setText("Associate Structure with Sequence");\r
- pdbFromFile.setText("From File");\r
- pdbFromFile.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbFromFile_actionPerformed();\r
- }\r
- });\r
- enterPDB.setText("Enter PDB Id");\r
- enterPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- enterPDB_actionPerformed();\r
- }\r
- });\r
- discoverPDB.setText("Discover PDB ids");\r
- discoverPDB.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- discoverPDB_actionPerformed();\r
- }\r
- });\r
- outputMenu.setText("Output to Textbox...");\r
- sequenceFeature.setText("Create Sequence Feature");\r
- sequenceFeature.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- sequenceFeature_actionPerformed();\r
- }\r
- });\r
- textColour.setText("Text Colour");\r
- textColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- textColour_actionPerformed();\r
- }\r
- });\r
- jMenu1.setText("Group");\r
- structureMenu.setText("Structure");\r
- viewStructureMenu.setText("View Structure");\r
- // colStructureMenu.setText("Colour By Structure");\r
- editSequence.setText("Edit Sequence...");\r
- editSequence.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- editSequence_actionPerformed(actionEvent);\r
- }\r
- });\r
- /* annotationMenuItem.setText("By Annotation");\r
- annotationMenuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- annotationMenuItem_actionPerformed(actionEvent);\r
- }\r
- });*/\r
-\r
- add(groupMenu);\r
-\r
- add(sequenceMenu);\r
- this.add(structureMenu);\r
- groupMenu.add(editMenu);\r
- groupMenu.add(outputMenu);\r
- groupMenu.add(sequenceFeature);\r
- groupMenu.add(jMenu1);\r
- sequenceMenu.add(sequenceName);\r
- colourMenu.add(textColour);\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideMenuItem);\r
- colourMenu.add(userDefinedColour);\r
-\r
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
- {\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- JMenuItem item = new JMenuItem(userColours.\r
- nextElement().toString());\r
- item.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- userDefinedColour_actionPerformed(evt);\r
- }\r
- });\r
- colourMenu.add(item);\r
- }\r
- }\r
-\r
- colourMenu.addSeparator();\r
- colourMenu.add(abovePIDColour);\r
- colourMenu.add(conservationMenuItem);\r
- //colourMenu.add(annotationMenuItem);\r
- editMenu.add(copy);\r
- editMenu.add(cut);\r
- editMenu.add(editSequence);\r
- editMenu.add(upperCase);\r
- editMenu.add(lowerCase);\r
- editMenu.add(toggle);\r
- pdbMenu.add(pdbFromFile);\r
- pdbMenu.add(enterPDB);\r
- pdbMenu.add(discoverPDB);\r
- jMenu1.add(groupName);\r
- jMenu1.add(unGroupMenuItem);\r
- jMenu1.add(colourMenu);\r
- jMenu1.add(showBoxes);\r
- jMenu1.add(showText);\r
- jMenu1.add(showColourText);\r
- jMenu1.add(outline);\r
- structureMenu.add(pdbMenu);\r
- structureMenu.add(viewStructureMenu);\r
- // structureMenu.add(colStructureMenu);\r
- noColourmenuItem.setText("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed();\r
- }\r
- });\r
-\r
- clustalColour.setText("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed();\r
- }\r
- });\r
- zappoColour.setText("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed();\r
- }\r
- });\r
- taylorColour.setText("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed();\r
- }\r
- });\r
- hydrophobicityColour.setText("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed();\r
- }\r
- });\r
- helixColour.setText("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed();\r
- }\r
- });\r
- strandColour.setText("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed();\r
- }\r
- });\r
- turnColour.setText("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed();\r
- }\r
- });\r
- buriedColour.setText("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed();\r
- }\r
- });\r
- abovePIDColour.setText("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed();\r
- }\r
- });\r
- userDefinedColour.setText("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setText("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed();\r
- }\r
- });\r
- BLOSUM62Colour.setText("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed();\r
- }\r
- });\r
- conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed();\r
- }\r
- });\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- void refresh()\r
- {\r
- ap.paintAlignment(true);\r
-\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void clustalColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
- ap.av.alignment.getWidth());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void zappoColour_actionPerformed()\r
- {\r
- getGroup().cs = new ZappoColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void taylorColour_actionPerformed()\r
- {\r
- getGroup().cs = new TaylorColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void hydrophobicityColour_actionPerformed()\r
- {\r
- getGroup().cs = new HydrophobicColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void helixColour_actionPerformed()\r
- {\r
- getGroup().cs = new HelixColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void strandColour_actionPerformed()\r
- {\r
- getGroup().cs = new StrandColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void turnColour_actionPerformed()\r
- {\r
- getGroup().cs = new TurnColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void buriedColour_actionPerformed()\r
- {\r
- getGroup().cs = new BuriedColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void nucleotideMenuItem_actionPerformed()\r
- {\r
- getGroup().cs = new NucleotideColourScheme();\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void abovePIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (abovePIDColour.isSelected())\r
- {\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
- getGroup().getName());\r
-\r
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
-\r
- SliderPanel.showPIDSlider();\r
- }\r
- else // remove PIDColouring\r
- {\r
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- if (e.getActionCommand().equals("User Defined..."))\r
- {\r
- new UserDefinedColours(ap, sg);\r
- }\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
-\r
- sg.cs = udc;\r
- }\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void PIDColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void BLOSUM62Colour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
-\r
- sg.cs = new Blosum62ColourScheme();\r
-\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1));\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void noColourmenuItem_actionPerformed()\r
- {\r
- getGroup().cs = null;\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void conservationMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg.cs == null)\r
- {\r
- return;\r
- }\r
-\r
- if (conservationMenuItem.isSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(ap.av.\r
- hiddenRepSequences),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
-\r
- sg.cs.setConservation(c);\r
-\r
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
- SliderPanel.showConservationSlider();\r
- }\r
- else // remove ConservationColouring\r
- {\r
- sg.cs.setConservation(null);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(\r
- sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);\r
-\r
- acg.predefinedColours = true;\r
- sg.cs = acg;\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void groupName_actionPerformed()\r
- {\r
-\r
- SequenceGroup sg = getGroup();\r
- EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
- sg.getDescription(),\r
- " Group Name ",\r
- "Group Description ",\r
- "Edit Group Name/Description");\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(dialog.getName());\r
- sg.setDescription(dialog.getDescription());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- SequenceGroup getGroup()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- // this method won't add a new group if it already exists\r
- if (sg != null)\r
- {\r
- ap.av.alignment.addGroup(sg);\r
- }\r
-\r
- return sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void sequenceName_actionPerformed()\r
- {\r
- EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
- sequence.getDescription(),\r
- " Sequence Name ",\r
- "Sequence Description ",\r
- "Edit Sequence Name/Description");\r
-\r
- if (!dialog.accept)\r
- {\r
- return;\r
- }\r
-\r
- if (dialog.getName() != null)\r
- {\r
- if (dialog.getName().indexOf(" ") > -1)\r
- {\r
- JOptionPane.showMessageDialog(ap,\r
- "Spaces have been converted to \"_\"",\r
- "No spaces allowed in Sequence Name",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
-\r
- sequence.setName(dialog.getName().replace(' ', '_'));\r
- ap.paintAlignment(false);\r
- }\r
-\r
- sequence.setDescription(dialog.getDescription());\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void unGroupMenuItem_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void outline_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
- Color.BLUE);\r
-\r
- if (col != null)\r
- {\r
- sg.setOutlineColour(col);\r
- }\r
-\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showBoxes_actionPerformed()\r
- {\r
- getGroup().setDisplayBoxes(showBoxes.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showText_actionPerformed()\r
- {\r
- getGroup().setDisplayText(showText.isSelected());\r
- refresh();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void showColourText_actionPerformed()\r
- {\r
- getGroup().setColourText(showColourText.isSelected());\r
- refresh();\r
- }\r
-\r
- public void showLink(String url)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher.openURL(url);\r
- }\r
- catch (Exception ex)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Unixers: Couldn't find default web browser."\r
- +\r
- "\nAdd the full path to your browser in Preferences.",\r
- "Web browser not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- void hideSequences(boolean representGroup)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null || sg.getSize() < 1)\r
- {\r
- ap.av.hideSequence(new SequenceI[]\r
- {sequence});\r
- return;\r
- }\r
-\r
- ap.av.setSelectionGroup(null);\r
-\r
- if (representGroup)\r
- {\r
- ap.av.hideRepSequences(sequence, sg);\r
-\r
- return;\r
- }\r
-\r
- int gsize = sg.getSize();\r
- SequenceI[] hseqs;\r
-\r
- hseqs = new SequenceI[gsize];\r
-\r
- int index = 0;\r
- for (int i = 0; i < gsize; i++)\r
- {\r
- hseqs[index++] = sg.getSequenceAt(i);\r
- }\r
-\r
- ap.av.hideSequence(hseqs);\r
- }\r
-\r
- public void copy_actionPerformed()\r
- {\r
- ap.alignFrame.copy_actionPerformed(null);\r
- }\r
-\r
- public void cut_actionPerformed()\r
- {\r
- ap.alignFrame.cut_actionPerformed(null);\r
- }\r
-\r
- void changeCase(ActionEvent e)\r
- {\r
- Object source = e.getSource();\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if (sg != null)\r
- {\r
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(\r
- sg.getStartRes(), sg.getEndRes() + 1);\r
-\r
- String description;\r
- int caseChange;\r
-\r
- if (source == toggle)\r
- {\r
- description = "Toggle Case";\r
- caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
- }\r
- else if (source == upperCase)\r
- {\r
- description = "To Upper Case";\r
- caseChange = ChangeCaseCommand.TO_UPPER;\r
- }\r
- else\r
- {\r
- description = "To Lower Case";\r
- caseChange = ChangeCaseCommand.TO_LOWER;\r
- }\r
-\r
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- startEnd, caseChange\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(caseCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
-\r
- }\r
- }\r
-\r
- public void outputText_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- cap.setForInput(null);\r
- Desktop.addInternalFrame(cap,\r
- "Alignment output - " + e.getActionCommand(), 600,\r
- 500);\r
-\r
- String[] omitHidden = null;\r
-\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- System.out.println("PROMPT USER HERE");\r
- omitHidden = ap.av.getViewAsString(true);\r
- }\r
-\r
- cap.setText(new FormatAdapter().formatSequences(\r
- e.getActionCommand(),\r
- ap.av.getSelectionAsNewSequence(),\r
- omitHidden));\r
- }\r
-\r
- public void pdbFromFile_actionPerformed()\r
- {\r
- jalview.io.JalviewFileChooser chooser\r
- = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Select a PDB file");\r
- chooser.setToolTipText("Load a PDB file");\r
-\r
- int value = chooser.showOpenDialog(null);\r
-\r
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- try\r
- {\r
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
- jalview.io.AppletFormatAdapter.FILE);\r
-\r
- if (pdbfile.id == null)\r
- {\r
- String reply = JOptionPane.showInternalInputDialog(\r
- Desktop.desktop,\r
- "Couldn't find a PDB id in the file supplied."\r
- + "Please enter an Id to identify this structure.",\r
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- entry.setId(reply);\r
- }\r
- else\r
- {\r
- entry.setId(pdbfile.id);\r
- }\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- entry.setFile(choice);\r
- sequence.getDatasetSequence().addPDBId(entry);\r
- }\r
-\r
- }\r
-\r
- public void enterPDB_actionPerformed()\r
- {\r
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (id != null && id.length() > 0)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(id.toUpperCase());\r
- sequence.getDatasetSequence()\r
- .addPDBId(entry);\r
- }\r
- }\r
-\r
- public void discoverPDB_actionPerformed()\r
- {\r
- SequenceI[] sequences =\r
- ap.av.selectionGroup == null ?\r
- new Sequence[]{sequence}\r
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);\r
-\r
- new jalview.io.DBRefFetcher(sequences,\r
- ap.alignFrame).fetchDBRefs(false);\r
- }\r
-\r
- public void sequenceFeature_actionPerformed()\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
- {\r
- return;\r
- }\r
-\r
- int gSize = sg.getSize();\r
- SequenceI[] seqs = new SequenceI[gSize];\r
- SequenceFeature[] features = new SequenceFeature[gSize];\r
-\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
- int end = sg.findEndRes(sg.getSequenceAt(i));\r
- features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
- }\r
-\r
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .amendFeatures(seqs, features, true, ap))\r
- {\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- ap.av.setShowSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
- }\r
-\r
- public void textColour_actionPerformed()\r
- {\r
- SequenceGroup sg = getGroup();\r
- if (sg != null)\r
- {\r
- new TextColourChooser().chooseColour(ap, sg);\r
- }\r
- }\r
-\r
- public void colourByStructure(String pdbid)\r
- {\r
- Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
- .colourSequenceFromStructure(sequence, pdbid);\r
-\r
- AlignmentAnnotation an = new AlignmentAnnotation(\r
- "Structure", "Coloured by "+pdbid, anots);\r
-\r
- ap.av.alignment.addAnnotation(an);\r
- an.createSequenceMapping(sequence, 0, true);\r
- //an.adjustForAlignment();\r
- ap.av.alignment.setAnnotationIndex(an,0);\r
-\r
- ap.adjustAnnotationHeight();\r
-\r
- sequence.addAlignmentAnnotation(an);\r
-\r
- }\r
-\r
- public void editSequence_actionPerformed(ActionEvent actionEvent)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if(sg!=null)\r
- {\r
- if (sequence == null)\r
- sequence = (Sequence) sg.getSequenceAt(0);\r
-\r
- EditNameDialog dialog = new EditNameDialog(\r
- sequence.getSequenceAsString(\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1),\r
- null,\r
- "Edit Sequence ",\r
- null,\r
- "Edit Sequence");\r
-\r
- if (dialog.accept)\r
- {\r
- EditCommand editCommand = new EditCommand(\r
- "Edit Sequences", EditCommand.REPLACE,\r
- dialog.getName().replace(' ', ap.av.getGapCharacter()),\r
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
- sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment\r
- );\r
-\r
- ap.alignFrame.addHistoryItem(editCommand);\r
-\r
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- }\r
- }\r
- }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import MCview.*;
+import jalview.analysis.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PopupMenu
+ extends JPopupMenu
+{
+ JMenu groupMenu = new JMenu();
+ JMenuItem groupName = new JMenuItem();
+ protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour = new
+ JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+ protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ AlignmentPanel ap;
+ JMenu sequenceMenu = new JMenu();
+ JMenuItem sequenceName = new JMenuItem();
+ Sequence sequence;
+ JMenuItem unGroupMenuItem = new JMenuItem();
+ JMenuItem outline = new JMenuItem();
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+ JMenu colourMenu = new JMenu();
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+ JMenu editMenu = new JMenu();
+ JMenuItem cut = new JMenuItem();
+ JMenuItem copy = new JMenuItem();
+ JMenuItem upperCase = new JMenuItem();
+ JMenuItem lowerCase = new JMenuItem();
+ JMenuItem toggle = new JMenuItem();
+ JMenu pdbMenu = new JMenu();
+ JMenuItem pdbFromFile = new JMenuItem();
+ JMenuItem enterPDB = new JMenuItem();
+ JMenuItem discoverPDB = new JMenuItem();
+ JMenu outputMenu = new JMenu();
+ JMenuItem sequenceFeature = new JMenuItem();
+ JMenuItem textColour = new JMenuItem();
+ JMenu jMenu1 = new JMenu();
+ JMenu structureMenu = new JMenu();
+ JMenu viewStructureMenu = new JMenu();
+ // JMenu colStructureMenu = new JMenu();
+ JMenuItem editSequence = new JMenuItem();
+ // JMenuItem annotationMenuItem = new JMenuItem();
+
+ /**
+ * Creates a new PopupMenu object.
+ *
+ * @param ap DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ {
+ ///////////////////////////////////////////////////////////
+ // If this is activated from the sequence panel, the user may want to
+ // edit or annotate a particular residue. Therefore display the residue menu
+ //
+ // If from the IDPanel, we must display the sequence menu
+ //////////////////////////////////////////////////////////
+ this.ap = ap;
+ sequence = seq;
+
+ ButtonGroup colours = new ButtonGroup();
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(abovePIDColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+
+ for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ {
+ JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
+ i]);
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outputText_actionPerformed(e);
+ }
+ });
+
+ outputMenu.add(item);
+ }
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ if (seq != null)
+ {
+ sequenceMenu.setText(sequence.getName());
+
+ JMenuItem menuItem;
+ if (seq.getDatasetSequence().getPDBId() != null
+ && seq.getDatasetSequence().getPDBId().size()>0)
+ {
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+ elements();
+
+ while (e.hasMoreElements())
+ {
+ final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+ menuItem = new JMenuItem();
+ menuItem.setText(pdb.getId());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ Vector seqs = new Vector();
+ for (int i = 0; i < ap.av.alignment.getHeight(); i++)
+ {
+ Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
+ if(pdbs==null)
+ continue;
+
+ for(int p=0; p<pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
+ if(p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
+ seqs.addElement(ap.av.alignment.getSequenceAt(i));
+
+ continue;
+ }
+ }
+ }
+
+ SequenceI [] seqs2 = new SequenceI[seqs.size()];
+ seqs.toArray(seqs2);
+
+ new AppJmol(pdb, seqs2, null, ap);
+ // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+
+ /* menuItem = new JMenuItem();
+ menuItem.setText(pdb.getId());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ colourByStructure(pdb.getId());
+ }
+ });
+ colStructureMenu.add(menuItem);*/
+ }
+ }
+ else
+ {
+ structureMenu.remove(viewStructureMenu);
+ // structureMenu.remove(colStructureMenu);
+ }
+
+ menuItem = new JMenuItem("Hide Sequences");
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(false);
+ }
+ });
+ add(menuItem);
+
+ if (ap.av.getSelectionGroup() != null
+ && ap.av.getSelectionGroup().getSize() > 1)
+ {
+ menuItem = new JMenuItem("Represent Group with " + seq.getName());
+ menuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSequences(true);
+ }
+ });
+ sequenceMenu.add(menuItem);
+ }
+
+ if (ap.av.hasHiddenRows)
+ {
+ final int index = ap.av.alignment.findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index) -
+ ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ menuItem = new JMenuItem("Reveal Sequences");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showSequence(index);
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+ add(menuItem);
+ }
+
+ menuItem = new JMenuItem("Reveal All");
+ menuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ap.av.showAllHiddenSeqs();
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+ });
+
+ add(menuItem);
+ }
+
+ }
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ groupName.setText(sg.getName());
+
+ if (sg.cs instanceof ZappoColourScheme)
+ {
+ zappoColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TaylorColourScheme)
+ {
+ taylorColour.setSelected(true);
+ }
+ else if (sg.cs instanceof PIDColourScheme)
+ {
+ PIDColour.setSelected(true);
+ }
+ else if (sg.cs instanceof Blosum62ColourScheme)
+ {
+ BLOSUM62Colour.setSelected(true);
+ }
+ else if (sg.cs instanceof UserColourScheme)
+ {
+ userDefinedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HydrophobicColourScheme)
+ {
+ hydrophobicityColour.setSelected(true);
+ }
+ else if (sg.cs instanceof HelixColourScheme)
+ {
+ helixColour.setSelected(true);
+ }
+ else if (sg.cs instanceof StrandColourScheme)
+ {
+ strandColour.setSelected(true);
+ }
+ else if (sg.cs instanceof TurnColourScheme)
+ {
+ turnColour.setSelected(true);
+ }
+ else if (sg.cs instanceof BuriedColourScheme)
+ {
+ buriedColour.setSelected(true);
+ }
+ else if (sg.cs instanceof ClustalxColourScheme)
+ {
+ clustalColour.setSelected(true);
+ }
+ else
+ {
+ noColourmenuItem.setSelected(true);
+ }
+
+ if (sg.cs != null && sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+
+ showText.setSelected(sg.getDisplayText());
+ showColourText.setSelected(sg.getColourText());
+ showBoxes.setSelected(sg.getDisplayBoxes());
+ }
+ else
+ {
+ groupMenu.setVisible(false);
+ editMenu.setVisible(false);
+ }
+
+ if (!ap.av.alignment.getGroups().contains(sg))
+ {
+ unGroupMenuItem.setVisible(false);
+ }
+
+ if (seq == null)
+ {
+ sequenceMenu.setVisible(false);
+ structureMenu.setVisible(false);
+ }
+
+ if (links != null && links.size() > 0)
+ {
+ JMenu linkMenu = new JMenu("Link");
+ JMenuItem item;
+ for (int i = 0; i < links.size(); i++)
+ {
+ String link = links.elementAt(i).toString();
+ final String label = link.substring(0, link.indexOf("|"));
+ item = new JMenuItem(label);
+ final String url;
+
+ if (link.indexOf("$SEQUENCE_ID$") > -1)
+ {
+ String id = seq.getName();
+ if (id.indexOf("|") > -1)
+ {
+ id = id.substring(id.lastIndexOf("|") + 1);
+ }
+
+ url = link.substring(link.indexOf("|") + 1,
+ link.indexOf("$SEQUENCE_ID$"))
+ + id +
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+ }
+ else
+ {
+ url = link.substring(link.lastIndexOf("|") + 1);
+ }
+
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showLink(url);
+ }
+ });
+
+ linkMenu.add(item);
+ }
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception DOCUMENT ME!
+ */
+ private void jbInit()
+ throws Exception
+ {
+ groupMenu.setText("Group");
+ groupMenu.setText("Selection");
+ groupName.setText("Name");
+ groupName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed();
+ }
+ });
+ sequenceMenu.setText("Sequence");
+ sequenceName.setText("Edit Name/Description");
+ sequenceName.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed();
+ }
+ });
+ PIDColour.setFocusPainted(false);
+ unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+ });
+
+ outline.setText("Border colour");
+ outline.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed();
+ }
+ });
+ nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideMenuItem_actionPerformed();
+ }
+ });
+ colourMenu.setText("Group Colour");
+ showBoxes.setText("Boxes");
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed();
+ }
+ });
+ showText.setText("Text");
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed();
+ }
+ });
+ showColourText.setText("Colour Text");
+ showColourText.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed();
+ }
+ });
+ editMenu.setText("Edit");
+ cut.setText("Cut");
+ cut.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed();
+ }
+ });
+ upperCase.setText("To Upper Case");
+ upperCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ copy.setText("Copy");
+ copy.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed();
+ }
+ });
+ lowerCase.setText("To Lower Case");
+ lowerCase.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ toggle.setText("Toggle Case");
+ toggle.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ pdbMenu.setText("Associate Structure with Sequence");
+ pdbFromFile.setText("From File");
+ pdbFromFile.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ });
+ enterPDB.setText("Enter PDB Id");
+ enterPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ enterPDB_actionPerformed();
+ }
+ });
+ discoverPDB.setText("Discover PDB ids");
+ discoverPDB.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ discoverPDB_actionPerformed();
+ }
+ });
+ outputMenu.setText("Output to Textbox...");
+ sequenceFeature.setText("Create Sequence Feature");
+ sequenceFeature.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceFeature_actionPerformed();
+ }
+ });
+ textColour.setText("Text Colour");
+ textColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+ jMenu1.setText("Group");
+ structureMenu.setText("Structure");
+ viewStructureMenu.setText("View Structure");
+ // colStructureMenu.setText("Colour By Structure");
+ editSequence.setText("Edit Sequence...");
+ editSequence.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ editSequence_actionPerformed(actionEvent);
+ }
+ });
+ /* annotationMenuItem.setText("By Annotation");
+ annotationMenuItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ annotationMenuItem_actionPerformed(actionEvent);
+ }
+ });*/
+
+ add(groupMenu);
+
+ add(sequenceMenu);
+ this.add(structureMenu);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputMenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(jMenu1);
+ sequenceMenu.add(sequenceName);
+ colourMenu.add(textColour);
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(userDefinedColour);
+
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ JMenuItem item = new JMenuItem(userColours.
+ nextElement().toString());
+ item.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
+ colourMenu.add(item);
+ }
+ }
+
+ colourMenu.addSeparator();
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationMenuItem);
+ //colourMenu.add(annotationMenuItem);
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ pdbMenu.add(pdbFromFile);
+ pdbMenu.add(enterPDB);
+ pdbMenu.add(discoverPDB);
+ jMenu1.add(groupName);
+ jMenu1.add(unGroupMenuItem);
+ jMenu1.add(colourMenu);
+ jMenu1.add(showBoxes);
+ jMenu1.add(showText);
+ jMenu1.add(showColourText);
+ jMenu1.add(outline);
+ structureMenu.add(pdbMenu);
+ structureMenu.add(viewStructureMenu);
+ // structureMenu.add(colStructureMenu);
+ noColourmenuItem.setText("None");
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ });
+
+ clustalColour.setText("Clustalx colours");
+ clustalColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed();
+ }
+ });
+ zappoColour.setText("Zappo");
+ zappoColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed();
+ }
+ });
+ taylorColour.setText("Taylor");
+ taylorColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed();
+ }
+ });
+ hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
+ helixColour.setText("Helix propensity");
+ helixColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed();
+ }
+ });
+ strandColour.setText("Strand propensity");
+ strandColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed();
+ }
+ });
+ turnColour.setText("Turn propensity");
+ turnColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed();
+ }
+ });
+ buriedColour.setText("Buried Index");
+ buriedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed();
+ }
+ });
+ abovePIDColour.setText("Above % Identity");
+ abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed();
+ }
+ });
+ userDefinedColour.setText("User Defined...");
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour.setText("Percentage Identity");
+ PIDColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed();
+ }
+ });
+ BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ });
+ conservationMenuItem.setText("Conservation");
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ void refresh()
+ {
+ ap.paintAlignment(true);
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
+ ap.av.alignment.getWidth());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ZappoColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new TaylorColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new HydrophobicColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new HelixColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new StrandColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new TurnColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new BuriedColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new NucleotideColourScheme();
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void abovePIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (abovePIDColour.isSelected())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+ sg.getEndRes() + 1));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+ }
+ else // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
+ {
+ SequenceGroup sg = getGroup();
+
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(ap, sg);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ sg.cs = udc;
+ }
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new PIDColourScheme();
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+ hiddenRepSequences),
+ sg.getStartRes(),
+ sg.getEndRes() + 1));
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new Blosum62ColourScheme();
+
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+ hiddenRepSequences),
+ sg.getStartRes(),
+ sg.getEndRes() + 1));
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void conservationMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (conservationMenuItem.isSelected())
+ {
+ Conservation c = new Conservation("Group",
+ ResidueProperties.propHash, 3,
+ sg.getSequences(ap.av.
+ hiddenRepSequences),
+ sg.getStartRes(),
+ sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, ap.av.ConsPercGaps);
+
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ }
+
+ refresh();
+ }
+
+ public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ AnnotationColourGradient acg = new AnnotationColourGradient(
+ sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+
+ acg.predefinedColours = true;
+ sg.cs = acg;
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void groupName_actionPerformed()
+ {
+
+ SequenceGroup sg = getGroup();
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
+ sg.getDescription(),
+ " Group Name ",
+ "Group Description ",
+ "Edit Group Name/Description");
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ // this method won't add a new group if it already exists
+ if (sg != null)
+ {
+ ap.av.alignment.addGroup(sg);
+ }
+
+ return sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ void sequenceName_actionPerformed()
+ {
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(),
+ " Sequence Name ",
+ "Sequence Description ",
+ "Edit Sequence Name/Description");
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JOptionPane.showMessageDialog(ap,
+ "Spaces have been converted to \"_\"",
+ "No spaces allowed in Sequence Name",
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false);
+ }
+
+ sequence.setDescription(dialog.getDescription());
+
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.alignment.deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ protected void outline_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color.BLUE);
+
+ if (col != null)
+ {
+ sg.setOutlineColour(col);
+ }
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showBoxes_actionPerformed()
+ {
+ getGroup().setDisplayBoxes(showBoxes.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showText_actionPerformed()
+ {
+ getGroup().setDisplayText(showText.isSelected());
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void showColourText_actionPerformed()
+ {
+ getGroup().setColourText(showColourText.isSelected());
+ refresh();
+ }
+
+ public void showLink(String url)
+ {
+ try
+ {
+ jalview.util.BrowserLauncher.openURL(url);
+ }
+ catch (Exception ex)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Unixers: Couldn't find default web browser."
+ +
+ "\nAdd the full path to your browser in Preferences.",
+ "Web browser not found",
+ JOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null || sg.getSize() < 1)
+ {
+ ap.av.hideSequence(new SequenceI[]
+ {sequence});
+ return;
+ }
+
+ ap.av.setSelectionGroup(null);
+
+ if (representGroup)
+ {
+ ap.av.hideRepSequences(sequence, sg);
+
+ return;
+ }
+
+ int gsize = sg.getSize();
+ SequenceI[] hseqs;
+
+ hseqs = new SequenceI[gsize];
+
+ int index = 0;
+ for (int i = 0; i < gsize; i++)
+ {
+ hseqs[index++] = sg.getSequenceAt(i);
+ }
+
+ ap.av.hideSequence(hseqs);
+ }
+
+ public void copy_actionPerformed()
+ {
+ ap.alignFrame.copy_actionPerformed(null);
+ }
+
+ public void cut_actionPerformed()
+ {
+ ap.alignFrame.cut_actionPerformed(null);
+ }
+
+ void changeCase(ActionEvent e)
+ {
+ Object source = e.getSource();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if (sg != null)
+ {
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ String description;
+ int caseChange;
+
+ if (source == toggle)
+ {
+ description = "Toggle Case";
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == upperCase)
+ {
+ description = "To Upper Case";
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
+ description = "To Lower Case";
+ caseChange = ChangeCaseCommand.TO_LOWER;
+ }
+
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+ startEnd, caseChange
+ );
+
+ ap.alignFrame.addHistoryItem(caseCommand);
+
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+
+ }
+ }
+
+ public void outputText_actionPerformed(ActionEvent e)
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ Desktop.addInternalFrame(cap,
+ "Alignment output - " + e.getActionCommand(), 600,
+ 500);
+
+ String[] omitHidden = null;
+
+ if (ap.av.hasHiddenColumns)
+ {
+ System.out.println("PROMPT USER HERE");
+ omitHidden = ap.av.getViewAsString(true);
+ }
+
+ cap.setText(new FormatAdapter().formatSequences(
+ e.getActionCommand(),
+ ap.av.getSelectionAsNewSequence(),
+ omitHidden));
+ }
+
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser
+ = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+ getProperty(
+ "LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle("Select a PDB file");
+ chooser.setToolTipText("Load a PDB file");
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ PDBEntry entry = new PDBEntry();
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ try
+ {
+ MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ if (pdbfile.id == null)
+ {
+ String reply = JOptionPane.showInternalInputDialog(
+ Desktop.desktop,
+ "Couldn't find a PDB id in the file supplied."
+ + "Please enter an Id to identify this structure.",
+ "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+ if (reply == null)
+ {
+ return;
+ }
+
+ entry.setId(reply);
+ }
+ else
+ {
+ entry.setId(pdbfile.id);
+ }
+ }
+ catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+
+ entry.setFile(choice);
+ sequence.getDatasetSequence().addPDBId(entry);
+ }
+
+ }
+
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+ if (id != null && id.length() > 0)
+ {
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id.toUpperCase());
+ sequence.getDatasetSequence()
+ .addPDBId(entry);
+ }
+ }
+
+ public void discoverPDB_actionPerformed()
+ {
+ SequenceI[] sequences =
+ ap.av.selectionGroup == null ?
+ new Sequence[]{sequence}
+ : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
+
+ new jalview.ws.DBRefFetcher(sequences,
+ ap.alignFrame).fetchDBRefs(false);
+ }
+
+ public void sequenceFeature_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ int gSize = sg.getSize();
+ SequenceI[] seqs = new SequenceI[gSize];
+ SequenceFeature[] features = new SequenceFeature[gSize];
+
+ for (int i = 0; i < gSize; i++)
+ {
+ seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+ int end = sg.findEndRes(sg.getSequenceAt(i));
+ features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
+ }
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .amendFeatures(seqs, features, true, ap))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ ap.av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ public void textColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg != null)
+ {
+ new TextColourChooser().chooseColour(ap, sg);
+ }
+ }
+
+ public void colourByStructure(String pdbid)
+ {
+ Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
+
+ AlignmentAnnotation an = new AlignmentAnnotation(
+ "Structure", "Coloured by "+pdbid, anots);
+
+ ap.av.alignment.addAnnotation(an);
+ an.createSequenceMapping(sequence, 0, true);
+ //an.adjustForAlignment();
+ ap.av.alignment.setAnnotationIndex(an,0);
+
+ ap.adjustAnnotationHeight();
+
+ sequence.addAlignmentAnnotation(an);
+
+ }
+
+ public void editSequence_actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ if(sg!=null)
+ {
+ if (sequence == null)
+ sequence = (Sequence) sg.getSequenceAt(0);
+
+ EditNameDialog dialog = new EditNameDialog(
+ sequence.getSequenceAsString(
+ sg.getStartRes(),
+ sg.getEndRes() + 1),
+ null,
+ "Edit Sequence ",
+ null,
+ "Edit Sequence");
+
+ if (dialog.accept)
+ {
+ EditCommand editCommand = new EditCommand(
+ "Edit Sequences", EditCommand.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
+ );
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ }
+ }
+
+
+}
}
String lastMessage;
- public void mouseOverSequence(SequenceI sequence, int index)
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
- String tmp = sequence.hashCode()+" "+index+"";
+ String tmp = sequence.hashCode()+" "+index+" "+pos;
if (lastMessage == null || !lastMessage.equals(tmp))
{
// System.err.println("mouseOver Sequence: "+tmp);
- ssm.mouseOverSequence(sequence, index);
+ ssm.mouseOverSequence(sequence, index, pos);
}
lastMessage = tmp;
}
pos = setStatusMessage(sequence, res, seq);
if (ssm != null && pos>-1)
- mouseOverSequence(sequence, pos);
+ mouseOverSequence(sequence, res, pos);
tooltipText.setLength(6); // Cuts the buffer back to <html>
-/*\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.gui;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import MCview.*;\r
-import jalview.datamodel.*;\r
-import jalview.datamodel.xdb.embl.*;\r
-import java.io.File;\r
-import jalview.io.*;\r
-import java.awt.Rectangle;\r
-import java.awt.BorderLayout;\r
-import java.awt.Dimension;\r
-\r
-public class SequenceFetcher\r
-extends JPanel implements Runnable\r
-{\r
- JInternalFrame frame;\r
- AlignFrame alignFrame;\r
- StringBuffer result;\r
- final String noDbSelected = "-- Select Database --";\r
- public SequenceFetcher(AlignFrame af)\r
- {\r
- alignFrame = af;\r
- database.addItem(noDbSelected);\r
- database.addItem("Uniprot");\r
- database.addItem("EMBL");\r
- database.addItem("EMBLCDS");\r
- database.addItem("PDB");\r
- database.addItem("PFAM");\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
- }\r
- else\r
- {\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
- }\r
- }\r
-\r
- private String getFrameTitle()\r
- {\r
- return ( (alignFrame == null) ? "New " : "Additional ") +\r
- "Sequence Fetcher";\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(borderLayout2);\r
-\r
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
- jLabel1.setText(\r
- "Separate multiple accession ids with semi colon \";\"");\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed();\r
- }\r
- });\r
- close.setText("Close");\r
- close.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- close_actionPerformed(e);\r
- }\r
- });\r
- textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- textArea.setLineWrap(true);\r
- textArea.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent e)\r
- {\r
- if(e.getKeyCode()==KeyEvent.VK_ENTER)\r
- ok_actionPerformed();\r
- }\r
- });\r
- jPanel3.setLayout(borderLayout1);\r
- borderLayout1.setVgap(5);\r
- jPanel1.add(ok);\r
- jPanel1.add(close);\r
- jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);\r
- jPanel2.add(database);\r
- jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);\r
- jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);\r
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
- jScrollPane1.getViewport().add(textArea);\r
-\r
- }\r
-\r
- JComboBox database = new JComboBox();\r
- JLabel jLabel1 = new JLabel();\r
- JButton ok = new JButton();\r
- JButton close = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JTextArea textArea = new JTextArea();\r
- JScrollPane jScrollPane1 = new JScrollPane();\r
- JPanel jPanel2 = new JPanel();\r
- JPanel jPanel3 = new JPanel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- public void close_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- public void ok_actionPerformed()\r
- {\r
- database.setEnabled(false);\r
- textArea.setEnabled(false);\r
- ok.setEnabled(false);\r
- close.setEnabled(false);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- private void resetDialog()\r
- {\r
- database.setEnabled(true);\r
- textArea.setEnabled(true);\r
- ok.setEnabled(true);\r
- close.setEnabled(true);\r
- }\r
-\r
- public void run()\r
- {\r
- String error = "";\r
- if (database.getSelectedItem().equals(noDbSelected))\r
- {\r
- error += "Please select the source database\n";\r
- }\r
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
- textArea.setText(empty.replaceAll(textArea.getText()));\r
- if (textArea.getText().length() == 0)\r
- {\r
- error += "Please enter a (semi-colon separated list of) database id(s)";\r
- }\r
- if (error.length() > 0)\r
- {\r
- showErrorMessage(error);\r
- resetDialog();\r
- return;\r
- }\r
-\r
- result = new StringBuffer();\r
- if (database.getSelectedItem().equals("Uniprot"))\r
- {\r
- getUniprotFile(textArea.getText());\r
- }\r
- else if (database.getSelectedItem().equals("EMBL")\r
- || database.getSelectedItem().equals("EMBLCDS"))\r
- {\r
- String DBRefSource = database.getSelectedItem().equals("EMBLCDS")\r
- ? jalview.datamodel.DBRefSource.EMBLCDS\r
- : jalview.datamodel.DBRefSource.EMBL;\r
-\r
- StringTokenizer st = new StringTokenizer(textArea.getText(), ";");\r
- SequenceI[] seqs = null;\r
- while(st.hasMoreTokens())\r
- {\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
-\r
- File reply = dbFetch.fetchDataAsFile(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + st.nextToken(),\r
- "emblxml",null);\r
-\r
- jalview.datamodel.xdb.embl.EmblFile efile=null;\r
- if (reply != null && reply.exists())\r
- {\r
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
- }\r
- if (efile!=null) {\r
- for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {\r
- EmblEntry entry = (EmblEntry) i.next();\r
- SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);\r
- if (seqparts!=null) {\r
- SequenceI[] newseqs = null;\r
- int si=0;\r
- if (seqs==null) {\r
- newseqs = new SequenceI[seqparts.length];\r
- } else {\r
- newseqs = new SequenceI[seqs.length+seqparts.length];\r
-\r
- for (;si<seqs.length; si++) {\r
- newseqs[si] = seqs[si];\r
- seqs[si] = null;\r
- }\r
- }\r
- for (int j=0;j<seqparts.length; si++, j++) {\r
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer\r
- }\r
- seqs=newseqs;\r
-\r
- }\r
- }\r
- } else {\r
- result=null;\r
- }\r
- }\r
- if (seqs!=null && seqs.length>0) {\r
- if (parseResult(new Alignment(seqs), null, null)!=null)\r
- result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");\r
- }\r
- }\r
- else if (database.getSelectedItem().equals("PDB"))\r
- {\r
- StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");\r
- String query;\r
- SequenceI[] seqs = null;\r
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
- {\r
- SequenceI[] seqparts = getPDBFile(query.toUpperCase());\r
- if (seqparts != null)\r
- {\r
- if (seqs == null)\r
- {\r
- seqs = seqparts;\r
- }\r
- else\r
- {\r
- SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];\r
- int i=0;\r
- for (; i < seqs.length; i++)\r
- {\r
- newseqs[i] = seqs[i];\r
- seqs[i] = null;\r
- }\r
- for (int j=0;j<seqparts.length; i++, j++)\r
- {\r
- newseqs[i] = seqparts[j];\r
- }\r
- seqs=newseqs;\r
- }\r
- result.append("# Success for "+query.toUpperCase()+"\n");\r
- }\r
- }\r
- if (seqs != null && seqs.length > 0)\r
- {\r
- if (parseResult(new Alignment(seqs), null, null)!=null)\r
- {\r
- result.append(\r
- "# Successfully parsed the PDB File Queries into an Alignment");\r
- }\r
- }\r
- }\r
- else if( database.getSelectedItem().equals("PFAM"))\r
- {\r
- try\r
- {\r
- result.append(new FastaFile(\r
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
- + textArea.getText().toUpperCase(), "URL").print()\r
- );\r
-\r
- if(result.length()>0)\r
- {\r
- parseResult( result.toString(), textArea.getText().toUpperCase() );\r
- }\r
-\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- result = null;\r
- }\r
- }\r
-\r
- if (result == null || result.length() == 0)\r
- {\r
- showErrorMessage("Error retrieving " + textArea.getText()\r
- + " from " + database.getSelectedItem());\r
- }\r
-\r
- resetDialog();\r
- return;\r
- }\r
-\r
- void getUniprotFile(String id)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
-\r
- DBRefFetcher dbref = new DBRefFetcher();\r
- Vector entries = dbref.getUniprotEntries(file);\r
-\r
- if (entries != null)\r
- {\r
- //First, make the new sequences\r
- Enumeration en = entries.elements();\r
- while (en.hasMoreElements())\r
- {\r
- UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-\r
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
- en2 = entry.getName().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
-\r
- if (entry.getProtein() != null)\r
- {\r
- name.append(" " + entry.getProtein().getName().elementAt(0));\r
- }\r
-\r
- result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
- "\n");\r
-\r
- }\r
-\r
- //Then read in the features and apply them to the dataset\r
- Alignment al = parseResult(result.toString(), null);\r
- for (int i = 0; i < entries.size(); i++)\r
- {\r
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals("PDB"))\r
- {\r
- continue;\r
- }\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
-\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(\r
- DBRefSource.UNIPROT,\r
- "0",\r
- en2.nextElement().toString()));\r
- }\r
-\r
-\r
-\r
-\r
- al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);\r
- if (entry.getFeature() != null)\r
- {\r
- e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setFeatureGroup("Uniprot");\r
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- SequenceI[] getPDBFile(String id)\r
- {\r
- Vector result = new Vector();\r
- String chain = null;\r
- if (id.indexOf(":") > -1)\r
- {\r
- chain = id.substring(id.indexOf(":") + 1);\r
- id = id.substring(0, id.indexOf(":"));\r
- }\r
-\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").\r
- getAbsolutePath();\r
- if (file == null)\r
- {\r
- return null;\r
- }\r
- try\r
- {\r
- PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);\r
- for (int i = 0; i < pdbfile.chains.size(); i++)\r
- {\r
- if (chain == null ||\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
- toUpperCase().equals(chain))\r
- {\r
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);\r
- // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file\r
- SequenceI sq = pdbchain.sequence;\r
- // Specially formatted name for the PDB chain sequences retrieved from the PDB\r
- sq.setName("PDB|"+id+"|"+sq.getName());\r
- // Might need to add more metadata to the PDBEntry object\r
- // like below\r
- /*\r
- * PDBEntry entry = new PDBEntry();\r
- // Construct the PDBEntry\r
- entry.setId(id);\r
- if (entry.getProperty() == null)\r
- entry.setProperty(new Hashtable());\r
- entry.getProperty().put("chains",\r
- pdbchain.id\r
- + "=" + sq.getStart()\r
- + "-" + sq.getEnd());\r
- sq.getDatasetSequence().addPDBId(entry);\r
- */\r
- // Add PDB DB Refs\r
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
- DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,\r
- "0", id + pdbchain.id);\r
- sq.addDBRef(dbentry);\r
- // and add seuqence to the retrieved set\r
- result.addElement(sq.deriveSequence());\r
- }\r
- }\r
-\r
- if (result.size() < 1)\r
- {\r
- throw new Exception("WsDBFetch for PDB id resulted in zero result size");\r
- }\r
- }\r
- catch (Exception ex) // Problem parsing PDB file\r
- {\r
- jalview.bin.Cache.log.warn("Exception when retrieving " +\r
- textArea.getText() + " from " +\r
- database.getSelectedItem(), ex);\r
- return null;\r
- }\r
-\r
-\r
- SequenceI[] results = new SequenceI[result.size()];\r
- for (int i = 0, j = result.size(); i < j; i++)\r
- {\r
- results[i] = (SequenceI) result.elementAt(i);\r
- result.setElementAt(null,i);\r
- }\r
- return results;\r
- }\r
- Alignment parseResult(String result, String title)\r
- {\r
- String format = new IdentifyFile().Identify(result, "Paste");\r
- Alignment sequences = null;\r
- if (FormatAdapter.isValidFormat(format))\r
- {\r
- sequences = null;\r
- try\r
- {\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
- format);\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- if (sequences!=null)\r
- {\r
- return parseResult(sequences, title, format);\r
- }\r
- }\r
- else\r
- {\r
- showErrorMessage("Error retrieving " + textArea.getText()\r
- + " from " + database.getSelectedItem());\r
- }\r
-\r
- return null;\r
- }\r
-\r
- Alignment parseResult(Alignment al, String title, String currentFileFormat)\r
- {\r
-\r
- if (al != null && al.getHeight() > 0)\r
- {\r
- if (alignFrame == null)\r
- {\r
- AlignFrame af = new AlignFrame(al,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
- if (currentFileFormat!=null)\r
- {\r
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?\r
- }\r
-\r
- if(title==null)\r
- {\r
- title = "Retrieved from " + database.getSelectedItem();\r
- }\r
-\r
- Desktop.addInternalFrame(af,\r
- title,\r
- AlignFrame.DEFAULT_WIDTH,\r
- AlignFrame.DEFAULT_HEIGHT);\r
-\r
- af.statusBar.setText("Successfully pasted alignment file");\r
-\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- else\r
- {\r
- for (int i = 0; i < al.getHeight(); i++)\r
- {\r
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries\r
- }\r
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
- getHeight());\r
- alignFrame.viewport.alignment.getWidth();\r
- alignFrame.viewport.firePropertyChange("alignment", null,\r
- alignFrame.viewport.\r
- getAlignment().getSequences());\r
- }\r
- }\r
- return al;\r
- }\r
-\r
- void showErrorMessage(final String error)\r
- {\r
- resetDialog();\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- });\r
- }\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import MCview.*;
+import jalview.datamodel.*;
+import jalview.datamodel.xdb.embl.*;
+import java.io.File;
+import jalview.io.*;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.EBIFetchClient;
+
+import java.awt.Rectangle;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+public class SequenceFetcher
+extends JPanel implements Runnable
+{
+ jalview.ws.SequenceFetcher sfetch;
+ JInternalFrame frame;
+ AlignFrame alignFrame;
+ StringBuffer result;
+ final String noDbSelected = "-- Select Database --";
+ public SequenceFetcher(AlignFrame af)
+ {
+ alignFrame = af;
+ sfetch = new jalview.ws.SequenceFetcher();
+ database.addItem(noDbSelected);
+ /*
+ * Dynamically generated database list
+ * will need a translation function from
+ * internal source to externally distinct names.
+ * UNIPROT and UP_NAME are identical DB sources,
+ * and should be collapsed.
+ *
+
+ String dbs[] = sfetch.getSupportedDb();
+ for (int i=0; i<dbs.length;i++)
+ {
+ if (DBRefSource.isPrimaryDb(dbs[i]))
+ {
+ database.addItem(dbs[i]);
+ // should have some kind of human readable description of each database displayed when
+ * that combo is selected.
+ }
+ }*/
+ database.addItem("Uniprot");
+ database.addItem("EMBL");
+ database.addItem("EMBLCDS");
+ database.addItem("PDB");
+ database.addItem("PFAM");
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (System.getProperty("os.name").startsWith("Mac"))
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ }
+ }
+
+ private String getFrameTitle()
+ {
+ return ( (alignFrame == null) ? "New " : "Additional ") +
+ "Sequence Fetcher";
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ this.setLayout(borderLayout2);
+
+ database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(
+ "Separate multiple accession ids with semi colon \";\"");
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ close.setText("Close");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent e)
+ {
+ if(e.getKeyCode()==KeyEvent.VK_ENTER)
+ ok_actionPerformed();
+ }
+ });
+ jPanel3.setLayout(borderLayout1);
+ borderLayout1.setVgap(5);
+ jPanel1.add(ok);
+ jPanel1.add(close);
+ jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
+ jPanel2.add(database);
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
+ jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ jScrollPane1.getViewport().add(textArea);
+
+ }
+
+ JComboBox database = new JComboBox();
+ JLabel jLabel1 = new JLabel();
+ JButton ok = new JButton();
+ JButton close = new JButton();
+ JPanel jPanel1 = new JPanel();
+ JTextArea textArea = new JTextArea();
+ JScrollPane jScrollPane1 = new JScrollPane();
+ JPanel jPanel2 = new JPanel();
+ JPanel jPanel3 = new JPanel();
+ BorderLayout borderLayout1 = new BorderLayout();
+ BorderLayout borderLayout2 = new BorderLayout();
+ public void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {}
+ }
+
+ public void ok_actionPerformed()
+ {
+ database.setEnabled(false);
+ textArea.setEnabled(false);
+ ok.setEnabled(false);
+ close.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ private void resetDialog()
+ {
+ database.setEnabled(true);
+ textArea.setEnabled(true);
+ ok.setEnabled(true);
+ close.setEnabled(true);
+ }
+
+ public void run()
+ {
+ String error = "";
+ if (database.getSelectedItem().equals(noDbSelected))
+ {
+ error += "Please select the source database\n";
+ }
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ textArea.setText(empty.replaceAll(textArea.getText()));
+ if (textArea.getText().length() == 0)
+ {
+ error += "Please enter a (semi-colon separated list of) database id(s)";
+ }
+ if (error.length() > 0)
+ {
+ showErrorMessage(error);
+ resetDialog();
+ return;
+ }
+
+ result = new StringBuffer();
+ if (database.getSelectedItem().equals("Uniprot"))
+ {
+ getUniprotFile(textArea.getText());
+ }
+ else if (database.getSelectedItem().equals("EMBL")
+ || database.getSelectedItem().equals("EMBLCDS"))
+ {
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
+ ? jalview.datamodel.DBRefSource.EMBLCDS
+ : jalview.datamodel.DBRefSource.EMBL;
+
+ StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
+ SequenceI[] seqs = null;
+ while(st.hasMoreTokens())
+ {
+ EBIFetchClient dbFetch = new EBIFetchClient();
+
+ File reply = dbFetch.fetchDataAsFile(
+ database.getSelectedItem().toString().toLowerCase(
+ ) + ":" + st.nextToken(),
+ "emblxml",null);
+
+ jalview.datamodel.xdb.embl.EmblFile efile=null;
+ if (reply != null && reply.exists())
+ {
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
+ }
+ if (efile!=null) {
+ for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
+ EmblEntry entry = (EmblEntry) i.next();
+ SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
+ if (seqparts!=null) {
+ SequenceI[] newseqs = null;
+ int si=0;
+ if (seqs==null) {
+ newseqs = new SequenceI[seqparts.length];
+ } else {
+ newseqs = new SequenceI[seqs.length+seqparts.length];
+
+ for (;si<seqs.length; si++) {
+ newseqs[si] = seqs[si];
+ seqs[si] = null;
+ }
+ }
+ for (int j=0;j<seqparts.length; si++, j++) {
+ newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
+ }
+ seqs=newseqs;
+
+ }
+ }
+ } else {
+ result=null;
+ }
+ }
+ if (seqs!=null && seqs.length>0) {
+ if (parseResult(new Alignment(seqs), null, null)!=null)
+ result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
+ }
+ }
+ else if (database.getSelectedItem().equals("PDB"))
+ {
+ StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
+ String query;
+ SequenceI[] seqs = null;
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
+ {
+ SequenceI[] seqparts = getPDBFile(query.toUpperCase());
+ if (seqparts != null)
+ {
+ if (seqs == null)
+ {
+ seqs = seqparts;
+ }
+ else
+ {
+ SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
+ int i=0;
+ for (; i < seqs.length; i++)
+ {
+ newseqs[i] = seqs[i];
+ seqs[i] = null;
+ }
+ for (int j=0;j<seqparts.length; i++, j++)
+ {
+ newseqs[i] = seqparts[j];
+ }
+ seqs=newseqs;
+ }
+ result.append("# Success for "+query.toUpperCase()+"\n");
+ }
+ }
+ if (seqs != null && seqs.length > 0)
+ {
+ if (parseResult(new Alignment(seqs), null, null)!=null)
+ {
+ result.append(
+ "# Successfully parsed the PDB File Queries into an Alignment");
+ }
+ }
+ }
+ else if( database.getSelectedItem().equals("PFAM"))
+ {
+ try
+ {
+ result.append(new FastaFile(
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+ + textArea.getText().toUpperCase(), "URL").print()
+ );
+
+ if(result.length()>0)
+ {
+ parseResult( result.toString(), textArea.getText().toUpperCase() );
+ }
+
+ }
+ catch (java.io.IOException ex)
+ {
+ result = null;
+ }
+ }
+
+ if (result == null || result.length() == 0)
+ {
+ showErrorMessage("Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ }
+
+ resetDialog();
+ return;
+ }
+
+ void getUniprotFile(String id)
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+
+ DBRefFetcher dbref = new DBRefFetcher();
+ Vector entries = dbref.getUniprotEntries(file);
+
+ if (entries != null)
+ {
+ //First, make the new sequences
+ Enumeration en = entries.elements();
+ while (en.hasMoreElements())
+ {
+ UniprotEntry entry = (UniprotEntry) en.nextElement();
+
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
+ Enumeration en2 = entry.getAccession().elements();
+ while (en2.hasMoreElements())
+ {
+ name.append("|");
+ name.append(en2.nextElement());
+ }
+ en2 = entry.getName().elements();
+ while (en2.hasMoreElements())
+ {
+ name.append("|");
+ name.append(en2.nextElement());
+ }
+
+ if (entry.getProtein() != null)
+ {
+ name.append(" " + entry.getProtein().getName().elementAt(0));
+ }
+
+ result.append(name + "\n" + entry.getUniprotSequence().getContent() +
+ "\n");
+
+ }
+
+ //Then read in the features and apply them to the dataset
+ Alignment al = parseResult(result.toString(), null);
+ for (int i = 0; i < entries.size(); i++)
+ {
+ UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
+ Enumeration e = entry.getDbReference().elements();
+ Vector onlyPdbEntries = new Vector();
+ while (e.hasMoreElements())
+ {
+ PDBEntry pdb = (PDBEntry) e.nextElement();
+ if (!pdb.getType().equals("PDB"))
+ {
+ continue;
+ }
+
+ onlyPdbEntries.addElement(pdb);
+ }
+
+ Enumeration en2 = entry.getAccession().elements();
+ while (en2.hasMoreElements())
+ {
+ al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+ DBRefSource.UNIPROT,
+ "0",
+ en2.nextElement().toString()));
+ }
+
+
+
+
+ al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
+ if (entry.getFeature() != null)
+ {
+ e = entry.getFeature().elements();
+ while (e.hasMoreElements())
+ {
+ SequenceFeature sf = (SequenceFeature) e.nextElement();
+ sf.setFeatureGroup("Uniprot");
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
+ }
+ }
+ }
+ }
+ }
+
+ SequenceI[] getPDBFile(String id)
+ {
+ Vector result = new Vector();
+ String chain = null;
+ if (id.indexOf(":") > -1)
+ {
+ chain = id.substring(id.indexOf(":") + 1);
+ id = id.substring(0, id.indexOf(":"));
+ }
+
+ EBIFetchClient ebi = new EBIFetchClient();
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
+ getAbsolutePath();
+ if (file == null)
+ {
+ return null;
+ }
+ try
+ {
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
+ for (int i = 0; i < pdbfile.chains.size(); i++)
+ {
+ if (chain == null ||
+ ( (PDBChain) pdbfile.chains.elementAt(i)).id.
+ toUpperCase().equals(chain))
+ {
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
+ // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
+ SequenceI sq = pdbchain.sequence;
+ // Specially formatted name for the PDB chain sequences retrieved from the PDB
+ sq.setName("PDB|"+id+"|"+sq.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry();
+ // Construct the PDBEntry
+ entry.setId(id);
+ if (entry.getProperty() == null)
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("chains",
+ pdbchain.id
+ + "=" + sq.getStart()
+ + "-" + sq.getEnd());
+ sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
+ DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,
+ "0", id + pdbchain.id);
+ sq.addDBRef(dbentry);
+ // and add seuqence to the retrieved set
+ result.addElement(sq.deriveSequence());
+ }
+ }
+
+ if (result.size() < 1)
+ {
+ throw new Exception("WsDBFetch for PDB id resulted in zero result size");
+ }
+ }
+ catch (Exception ex) // Problem parsing PDB file
+ {
+ jalview.bin.Cache.log.warn("Exception when retrieving " +
+ textArea.getText() + " from " +
+ database.getSelectedItem(), ex);
+ return null;
+ }
+
+
+ SequenceI[] results = new SequenceI[result.size()];
+ for (int i = 0, j = result.size(); i < j; i++)
+ {
+ results[i] = (SequenceI) result.elementAt(i);
+ result.setElementAt(null,i);
+ }
+ return results;
+ }
+ Alignment parseResult(String result, String title)
+ {
+ String format = new IdentifyFile().Identify(result, "Paste");
+ Alignment sequences = null;
+ if (FormatAdapter.isValidFormat(format))
+ {
+ sequences = null;
+ try
+ {
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+ format);
+ }
+ catch (Exception ex)
+ {}
+
+ if (sequences!=null)
+ {
+ return parseResult(sequences, title, format);
+ }
+ }
+ else
+ {
+ showErrorMessage("Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ }
+
+ return null;
+ }
+
+ Alignment parseResult(Alignment al, String title, String currentFileFormat)
+ {
+
+ if (al != null && al.getHeight() > 0)
+ {
+ if (alignFrame == null)
+ {
+ AlignFrame af = new AlignFrame(al,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat!=null)
+ {
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
+ }
+
+ if(title==null)
+ {
+ title = "Retrieved from " + database.getSelectedItem();
+ }
+
+ Desktop.addInternalFrame(af,
+ title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ af.statusBar.setText("Successfully pasted alignment file");
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ }
+ catch (Exception ex)
+ {}
+ }
+ else
+ {
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
+ }
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
+ getHeight());
+ alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.firePropertyChange("alignment", null,
+ alignFrame.viewport.
+ getAlignment().getSequences());
+ }
+ }
+ return al;
+ }
+
+ void showErrorMessage(final String error)
+ {
+ resetDialog();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ error, "Error Retrieving Data",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+}
+
return;
}
- if ( (node.left() == null) && (node.right() == null))
+ if ( (node.left() == null) && (node.right() == null)) // TODO: internal node
{
node.color = c;
JMenuItem vamsasStore = new JMenuItem();
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
+ protected JMenu showProducts = new JMenu();
public JMenuItem featureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
JMenuItem annotationColour = new JMenuItem();
extractScores_actionPerformed(e);
}
});
- extractScores.setVisible(false); // JBPNote: TODO: make gui for regex based score extraction
+ extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
+ showProducts.setText("Get Cross References");
+ /*showProducts.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ showProducts_actionPerformed(e);
+ }
+ });*/
featureSettings.setText("Feature Settings...");
featureSettings.addActionListener(new ActionListener()
{
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
+ calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
calculateMenu.addSeparator();
calculateMenu.add(extractScores);
selectMenu.add(deleteGroups);
}
+ protected void showProducts_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void buildSortByAnnotationScoresMenu()
{
}
-/*\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.structure;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public interface SequenceListener\r
-{\r
- public void mouseOverSequence(SequenceI sequence, int index);\r
-\r
- public void highlightSequence(jalview.datamodel.SearchResults results);\r
-\r
- public void updateColours(SequenceI sequence, int index);\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.structure;
+
+import jalview.datamodel.*;
+
+public interface SequenceListener
+{
+ public void mouseOverSequence(SequenceI sequence, int index, int pos);
+
+ public void highlightSequence(jalview.datamodel.SearchResults results);
+
+ public void updateColours(SequenceI sequence, int index);
+}
// pairs
- public void mouseOverSequence(SequenceI seq, int index)
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index)
{
boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
+ if (index==-1)
+ index=seq.findPosition(indexpos);
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
for (int j = 0; j < mappings.length; j++)
{
- if (mappings[j].sequence == seq)
+ if (mappings[j].sequence == seq || mappings[j].sequence==seq.getDatasetSequence())
{
atomNo = mappings[j].getAtomNum(index);
// hasSequenceListeners = results.getSize() > 0;
if (handlingVamsasMo)
{
+ // maybe have to resolve seq to a dataset seqeunce...
// add in additional direct sequence and/or dataset sequence
// highlighting
results.addResult(seq, index, index);
// DEBUG
//System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
// index);
- // pass the mouse over onto the VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, index);
+ // pass the mouse over and absolute position onto the VamsasListener(s)
+ ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, indexpos);
}
}
}
* handled
*/
boolean handlingVamsasMo = false;
-
+ long lastmsg=0;
/**
* as mouseOverSequence but only route event to SequenceListeners
*
* @param sequenceI
- * @param position
+ * @param position in an alignment sequence
*/
public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
{
handlingVamsasMo = true;
- mouseOverSequence(sequenceI, position);
- handlingVamsasMo = false;
+ long msg = sequenceI.hashCode()*(1+position);
+ if (lastmsg!=msg)
+ {
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1);
+ }
+ handlingVamsasMo = false;
}
public Annotation[] colourSequenceFromStructure(SequenceI seq,
git://source.jalview.org / jalview.git / commitdiff