X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6208597ccf09b274ca9abba08f577be79a55cbdd;hb=d10280f7592e21f1ed4d1030d3ece3e95f3b385b;hp=deba02119d6d7cbde62a6746f1a4be60115e4a17;hpb=cc6d26d2738c5854ef81ce6787d66564c2281220;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index deba021..6208597 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -43,6 +43,7 @@ import jalview.analysis.AlignmentUtils.MappingResult; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.NJTree; import jalview.api.AlignViewportI; +import jalview.api.ViewStyleI; import jalview.bin.Cache; import jalview.commands.CommandI; import jalview.datamodel.Alignment; @@ -59,12 +60,11 @@ import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; import jalview.util.MessageManager; -import jalview.util.StringUtils; import jalview.viewmodel.AlignmentViewport; import jalview.ws.params.AutoCalcSetting; -import java.awt.Color; import java.awt.Container; +import java.awt.Dimension; import java.awt.Font; import java.awt.Rectangle; import java.io.File; @@ -95,62 +95,27 @@ public class AlignViewport extends AlignmentViewport implements int endSeq; - boolean showJVSuffix = true; - - boolean showText = true; - - boolean showColourText = false; - - boolean showBoxes = true; - - boolean wrapAlignment = false; - - boolean renderGaps = true; SequenceAnnotationOrder sortAnnotationsBy = null; - int charHeight; - - int charWidth; - - boolean validCharWidth; - - int wrappedWidth; - Font font; - boolean seqNameItalics; - NJTree currentTree = null; - boolean scaleAboveWrapped = false; - - boolean scaleLeftWrapped = true; - - boolean scaleRightWrapped = true; - - boolean showHiddenMarkers = true; - boolean cursorMode = false; boolean antiAlias = false; - Rectangle explodedPosition; + private Rectangle explodedGeometry; String viewName; - boolean gatherViewsHere = false; + private boolean gatherViewsHere = false; private Deque historyList = new ArrayDeque(); private Deque redoList = new ArrayDeque(); - int thresholdTextColour = 0; - - Color textColour = Color.black; - - Color textColour2 = Color.white; - private AnnotationColumnChooser annotationColumnSelectionState; /** * Creates a new AlignViewport object. @@ -259,32 +224,46 @@ public class AlignViewport extends AlignmentViewport implements init(); } - void init() + private void applyViewProperties() { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; - antiAlias = Cache.getDefault("ANTI_ALIAS", false); - showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); + viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true)); setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true)); setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false)); - centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false); + setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false)); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); setPadGaps(Cache.getDefault("PAD_GAPS", true)); - shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true); - showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true); + setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true)); + setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); + viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); + viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); + viewStyle.setShowUnconserved(Cache + .getDefault("SHOW_UNCONSERVED", false)); + sortByTree = Cache.getDefault("SORT_BY_TREE", false); + followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); + sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( + Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache.getDefault( + Preferences.SHOW_AUTOCALC_ABOVE, false); + + } + + void init() + { + this.startRes = 0; + this.endRes = alignment.getWidth() - 1; + this.startSeq = 0; + this.endSeq = alignment.getHeight() - 1; + applyViewProperties(); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + ""); String fontSize = Cache.getDefault("FONT_SIZE", "10"); - seqNameItalics = Cache.getDefault("ID_ITALICS", true); - int style = 0; if (fontStyle.equals("bold")) @@ -296,7 +275,7 @@ public class AlignViewport extends AlignmentViewport implements style = 2; } - setFont(new Font(fontName, style, Integer.parseInt(fontSize))); + setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true); alignment .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0)); @@ -330,7 +309,7 @@ public class AlignViewport extends AlignmentViewport implements { globalColourScheme = UserDefinedColours.loadDefaultColours(); ((UserColourScheme) globalColourScheme).setThreshold(0, - getIgnoreGapsConsensus()); + isIgnoreGapsConsensus()); } if (globalColourScheme != null) @@ -338,31 +317,9 @@ public class AlignViewport extends AlignmentViewport implements globalColourScheme.setConsensus(hconsensus); } } - - wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false); - showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false); - sortByTree = Cache.getDefault("SORT_BY_TREE", false); - followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); - sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( - Preferences.SORT_ANNOTATIONS, - SequenceAnnotationOrder.NONE.name())); - showAutocalculatedAbove = Cache.getDefault( - Preferences.SHOW_AUTOCALC_ABOVE, false); } /** - * centre columnar annotation labels in displayed alignment annotation TODO: - * add to jalviewXML and annotation display settings - */ - boolean centreColumnLabels = false; - - private boolean showdbrefs; - - private boolean shownpfeats; - - // --------END Structure Conservation - - /** * get the consensus sequence as displayed under the PID consensus annotation * row. * @@ -506,105 +463,52 @@ public class AlignViewport extends AlignmentViewport implements return endSeq; } + boolean validCharWidth; + /** - * DOCUMENT ME! + * update view settings with the given font. You may need to call + * alignPanel.fontChanged to update the layout geometry * - * @param f - * DOCUMENT ME! + * @param setGrid + * when true, charWidth/height is set according to font mentrics */ - public void setFont(Font f) + public void setFont(Font f, boolean setGrid) { font = f; Container c = new Container(); java.awt.FontMetrics fm = c.getFontMetrics(font); - setCharHeight(fm.getHeight()); - setCharWidth(fm.charWidth('M')); - validCharWidth = true; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Font getFont() - { - return font; - } - - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setCharWidth(int w) - { - this.charWidth = w; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharWidth() - { - return charWidth; - } - - /** - * DOCUMENT ME! - * - * @param h - * DOCUMENT ME! - */ - public void setCharHeight(int h) - { - this.charHeight = h; - } + int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle + .getCharHeight(); + if (setGrid) + { + setCharHeight(fm.getHeight()); + setCharWidth(ww); + } + viewStyle.setFontName(font.getName()); + viewStyle.setFontStyle(font.getStyle()); + viewStyle.setFontSize(font.getSize()); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getCharHeight() - { - return charHeight; + validCharWidth = true; } - /** - * DOCUMENT ME! - * - * @param w - * DOCUMENT ME! - */ - public void setWrappedWidth(int w) + @Override + public void setViewStyle(ViewStyleI settingsForView) { - this.wrappedWidth = w; - } + super.setViewStyle(settingsForView); + setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(), + viewStyle.getFontSize()), false); - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getWrappedWidth() - { - return wrappedWidth; } - /** * DOCUMENT ME! * * @return DOCUMENT ME! */ - public AlignmentI getAlignment() + public Font getFont() { - return alignment; + return font; } /** @@ -631,101 +535,6 @@ public class AlignViewport extends AlignmentViewport implements /** * DOCUMENT ME! * - * @param state - * DOCUMENT ME! - */ - public void setWrapAlignment(boolean state) - { - wrapAlignment = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowText(boolean state) - { - showText = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setRenderGaps(boolean state) - { - renderGaps = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getColourText() - { - return showColourText; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setColourText(boolean state) - { - showColourText = state; - } - - /** - * DOCUMENT ME! - * - * @param state - * DOCUMENT ME! - */ - public void setShowBoxes(boolean state) - { - showBoxes = state; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getWrapAlignment() - { - return wrapAlignment; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowText() - { - return showText; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowBoxes() - { - return showBoxes; - } - - /** - * DOCUMENT ME! - * * @return DOCUMENT ME! */ public char getGapCharacter() @@ -779,110 +588,6 @@ public class AlignViewport extends AlignmentViewport implements } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getShowJVSuffix() - { - return showJVSuffix; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setShowJVSuffix(boolean b) - { - showJVSuffix = b; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleAboveWrapped() - { - return scaleAboveWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleLeftWrapped() - { - return scaleLeftWrapped; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean getScaleRightWrapped() - { - return scaleRightWrapped; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleAboveWrapped(boolean b) - { - scaleAboveWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleLeftWrapped(boolean b) - { - scaleLeftWrapped = b; - } - - /** - * DOCUMENT ME! - * - * @param b - * DOCUMENT ME! - */ - public void setScaleRightWrapped(boolean b) - { - scaleRightWrapped = b; - } - - public void setDataset(boolean b) - { - isDataset = b; - } - - public boolean isDataset() - { - return isDataset; - } - - public boolean getShowHiddenMarkers() - { - return showHiddenMarkers; - } - - public void setShowHiddenMarkers(boolean show) - { - showHiddenMarkers = show; - } - - /** * returns the visible column regions of the alignment * * @param selectedRegionOnly @@ -955,55 +660,6 @@ public class AlignViewport extends AlignmentViewport implements return false; } - public boolean getCentreColumnLabels() - { - return centreColumnLabels; - } - - public void setCentreColumnLabels(boolean centrecolumnlabels) - { - centreColumnLabels = centrecolumnlabels; - } - - /** - * enable or disable the display of Database Cross References in the sequence - * ID tooltip - */ - public void setShowDbRefs(boolean show) - { - showdbrefs = show; - } - - /** - * - * @return true if Database References are to be displayed on tooltips. - */ - public boolean isShowDbRefs() - { - return showdbrefs; - } - - /** - * - * @return true if Non-positional features are to be displayed on tooltips. - */ - public boolean isShowNpFeats() - { - return shownpfeats; - } - - /** - * enable or disable the display of Non-Positional sequence features in the - * sequence ID tooltip - * - * @param show - */ - public void setShowNpFeats(boolean show) - { - shownpfeats = show; - } - - /** * when set, view will scroll to show the highlighted position */ @@ -1340,6 +996,10 @@ public class AlignViewport extends AlignmentViewport implements { // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different + // JBPComment: title is a largely redundant parameter at the moment + // JBPComment: this really should be an 'insert/pre/append' controller + // JBPComment: but the DNA/Protein check makes it a bit more complex + // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with // this comment: // TODO: create undo object for this JAL-1101 @@ -1350,6 +1010,7 @@ public class AlignViewport extends AlignmentViewport implements */ if (getAlignment().isNucleotide() != al.isNucleotide()) { + // TODO: JAL-845 try a bit harder to link up imported sequences final Set sequenceNames = getAlignment().getSequenceNames(); sequenceNames.retainAll(al.getSequenceNames()); if (!sequenceNames.isEmpty()) // at least one sequence name in both @@ -1360,6 +1021,8 @@ public class AlignViewport extends AlignmentViewport implements } } } + // TODO: JAL-407 regardless of above - identical sequences (based on ID and + // provenance) should share the same dataset sequence for (int i = 0; i < al.getHeight(); i++) { @@ -1367,6 +1030,8 @@ public class AlignViewport extends AlignmentViewport implements } // TODO this call was done by SequenceFetcher but not FileLoader or // CutAndPasteTransfer. Is it needed? + // JBPComment: this repositions the view to show the new sequences + // JBPComment: so it is needed for UX setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -1463,6 +1128,8 @@ public class AlignViewport extends AlignmentViewport implements if (openSplitPane) { + // TODO: move this kind of constructor stuff to a factory/controller + // method ? /* * Open in split pane. DNA sequence above, protein below. */ @@ -1478,10 +1145,10 @@ public class AlignViewport extends AlignmentViewport implements cdnaFrame.setVisible(true); proteinFrame.setVisible(true); String sep = String.valueOf(File.separatorChar); - String proteinShortName = StringUtils.getLastToken( - proteinFrame.getTitle(), sep); - String dnaShortName = StringUtils.getLastToken(cdnaFrame.getTitle(), - sep); + String proteinShortName = proteinFrame.getTitle().substring( + proteinFrame.getTitle().lastIndexOf(sep) + 1); + String dnaShortName = cdnaFrame.getTitle().substring( + cdnaFrame.getTitle().lastIndexOf(sep) + 1); String linkedTitle = MessageManager.formatMessage( "label.linked_view_title", dnaShortName, proteinShortName); JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame); @@ -1520,4 +1187,39 @@ public class AlignViewport extends AlignmentViewport implements { this.annotationColumnSelectionState = currentAnnotationColumnSelectionState; } + + @Override + public void setIdWidth(int i) + { + super.setIdWidth(i); + AlignmentPanel ap = getAlignPanel(); + if (ap != null) + { + // modify GUI elements to reflect geometry change + Dimension idw = getAlignPanel().getIdPanel().getIdCanvas() + .getPreferredSize(); + idw.width = i; + getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw); + } + } + + public Rectangle getExplodedGeometry() + { + return explodedGeometry; + } + + public void setExplodedGeometry(Rectangle explodedPosition) + { + this.explodedGeometry = explodedPosition; + } + + public boolean isGatherViewsHere() + { + return gatherViewsHere; + } + + public void setGatherViewsHere(boolean gatherViewsHere) + { + this.gatherViewsHere = gatherViewsHere; + } }