From 2e6c07be1efbc95a6a59b4502c751042dcf6b0e7 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 24 Oct 2006 11:16:53 +0000 Subject: [PATCH] Commented out for compilation --- src/jalview/appletgui/APopupMenu.java | 4 +- src/jalview/appletgui/AlignFrame.java | 207 ++-------------------------- src/jalview/appletgui/FeatureRenderer.java | 8 +- src/jalview/appletgui/RedundancyPanel.java | 12 +- src/jalview/appletgui/SeqPanel.java | 8 -- 5 files changed, 27 insertions(+), 212 deletions(-) diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 853574b..4972874 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -232,7 +232,7 @@ public class APopupMenu else if(source==cut) ap.alignFrame.cut_actionPerformed(); else if(source==toUpper || source==toLower || source==toggleCase) - { + {/* SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null) { @@ -269,7 +269,7 @@ public class APopupMenu while (end < sg.getEndRes()); } ap.seqPanel.seqCanvas.repaint(); - } + }*/ } else outputText(evt); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 8e54ba9..b0e5715 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -23,6 +23,7 @@ import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; import jalview.io.*; +import jalview.commands.*; import java.awt.*; import java.awt.event.*; import java.util.*; @@ -668,68 +669,21 @@ public void itemStateChanged(ItemEvent evt) void updateEditMenuBar() { - if (historyList.size() > 0) - { - undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); - } - else - { - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - } - - if (redoList.size() > 0) - { - redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); - } - else - { - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - } } - public void addHistoryItem(HistoryItem hi) - { - historyList.push(hi); - redoList.removeAllElements(); - updateEditMenuBar(); - } protected void undoMenuItem_actionPerformed() { - HistoryItem nh,hi = (HistoryItem) historyList.pop(); - redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } protected void redoMenuItem_actionPerformed() { - HistoryItem nh,hi = (HistoryItem) redoList.pop(); - historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - if (hi.alColumnChanges!=null) - nh.alColumnChanges=hi.alColumnChanges.getInverse(); - restoreHistoryItem(hi); - updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + void restoreHistoryItem(CommandI command) { - hi.restore(viewport.getColumnSelection()); - updateEditMenuBar(); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void moveSelectedSequences(boolean up) @@ -882,8 +836,8 @@ public void itemStateChanged(ItemEvent evt) protected void pasteThis_actionPerformed() { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); + // addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, + // HistoryItem.PASTE)); paste(false); } @@ -970,8 +924,8 @@ public void itemStateChanged(ItemEvent evt) protected void delete_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); + //addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, + // HistoryItem.HIDE)); if (viewport.getSelectionGroup() == null) { return; @@ -1073,149 +1027,18 @@ public void itemStateChanged(ItemEvent evt) public void remove2LeftMenuItem_actionPerformed() { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); - edit.addShift(0, min); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } } public void remove2RightMenuItem_actionPerformed() { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveRight(max); - } - - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveRight(max)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } public void removeGappedColumnMenuItem_actionPerformed() { - HistoryItem edit; - addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - viewport.getAlignment().removeGaps(); - - viewport.setStartRes(seq.findIndex(startRes)-1); - - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences - // TODO: columnSelection.compensateforedits should be called (and passed to history item) - HistoryItem editgaps; - addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); - - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); - - SequenceI current; - Vector seqs=null; - - int start=0, end = viewport.alignment.getWidth(); - - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSequences(false) != null - && viewport.getSelectionGroup().getSize(false)>0) - { - seqs = viewport.getSelectionGroup().getSequences(true); - start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; - } - else - seqs = viewport.alignment.getSequences(); - - /* Commented out regions below are partial implementation of todo above. - * divide start,end into visible chunks, and for each: - int diff=end-start+1; - int diffmax=0; - int dr[] = new int[seqs.size()]; - */ - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - //dr[i]= - current.removeGaps(start, end); - /*if (d0) { - // record shift for history. - editgaps.addShift(start, diff); - if (viewport.hasHiddenColumns && diffmax>diff) { - // pad sequence - StringBuffer gaps=new StringBuffer(diffmax); - for (int i=0,j=diffmax-diff; i0) { - String sq = current.getSequence(); - current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); - } - } - } - }*/ - - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void alignmentChanged() @@ -1622,8 +1445,8 @@ public void itemStateChanged(ItemEvent evt) public void sortPairwiseMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); alignPanel.repaint(); @@ -1631,16 +1454,16 @@ public void itemStateChanged(ItemEvent evt) public void sortIDMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByID(viewport.getAlignment()); alignPanel.repaint(); } public void sortGroupMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByGroup(viewport.getAlignment()); alignPanel.repaint(); @@ -1786,8 +1609,8 @@ public void itemStateChanged(ItemEvent evt) { public void actionPerformed(ActionEvent evt) { - addHistoryItem(new HistoryItem("Sort", viewport.alignment, - HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); alignPanel.repaint(); } diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java index a24525e..954a95e 100755 --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -412,10 +412,10 @@ public class FeatureRenderer { void setTransparency(Graphics g, float value) { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, value)); + //Graphics2D g2 = (Graphics2D) g; + // g2.setComposite( + // AlphaComposite.getInstance( + // AlphaComposite.SRC_OVER, value)); } } diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java index 5037a50..7ceb570 100755 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -193,14 +193,14 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList } public void applyButton_actionPerformed() { - historyList.push(new HistoryItem("Remove redundancy", - ap.av.alignment, HistoryItem.HIDE)); + // historyList.push(new HistoryItem("Remove redundancy", + // ap.av.alignment, HistoryItem.HIDE)); if ((historyList.size() == 1) || !ap.alignFrame.historyList.contains(historyList.firstElement())) { - ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement()); - ap.alignFrame.updateEditMenuBar(); + // ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement()); + // ap.alignFrame.updateEditMenuBar(); } Vector del = new Vector(); @@ -243,8 +243,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList public void undoButton_actionPerformed() { - HistoryItem hi = (HistoryItem) historyList.pop(); - ap.alignFrame.restoreHistoryItem(hi); + // HistoryItem hi = (HistoryItem) historyList.pop(); + // ap.alignFrame.restoreHistoryItem(hi); if (historyList.size() == 0) { diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 7e5a207..8d42655 100755 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -246,8 +246,6 @@ public class SeqPanel void insertGapAtCursor(boolean group) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; @@ -257,8 +255,6 @@ public class SeqPanel void deleteGapAtCursor(boolean group) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); @@ -354,8 +350,6 @@ public class SeqPanel if(seq<0 || res<0) return; - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) @@ -472,8 +466,6 @@ public class SeqPanel public void doMousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem(new HistoryItem( - "Edit Sequence", av.alignment, HistoryItem.EDIT)); int seq = findSeq(evt); int res = findRes(evt); -- 1.7.10.2