From: tcofoegbu Date: Tue, 30 Jun 2015 11:42:25 +0000 (+0100) Subject: Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop X-Git-Tag: Release_2_10_0~585^2~10 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=7703a6a091c65e45bfb8f4d056cd2cbdb19b3535;hp=3f3c6c3a2b99fee2e726d18302af1b3320331212 Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop --- diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index ca1d158..eaf93c2 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -927,7 +927,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, : showForSequences); aa.visible = visible; } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); } private void setAnnotationSortOrder(SequenceAnnotationOrder order) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 01a22ed..d2e247f 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -5991,7 +5991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, aa.visible = visible; } } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); alignPanel.alignmentChanged(); } diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index fc889ad..cf82bfe 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -1027,13 +1027,13 @@ public class AlignViewport extends AlignmentViewport implements * is found, the result will be empty. */ SearchResults sr = new SearchResults(); - int seqOffset = findComplementScrollTarget(sr); + int verticalOffset = findComplementScrollTarget(sr); if (!sr.isEmpty()) { // TODO would like next line without cast but needs more refactoring... final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel(); complementPanel.setFollowingComplementScroll(true); - complementPanel.scrollToCentre(sr, seqOffset); + complementPanel.scrollToCentre(sr, verticalOffset); } } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 5bc46f4..7228e1b 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,6 +20,21 @@ */ package jalview.gui; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -27,6 +42,7 @@ import java.awt.Dimension; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Graphics; +import java.awt.Insets; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.print.PageFormat; @@ -41,21 +57,6 @@ import java.util.List; import javax.swing.SwingUtilities; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.MessageManager; - /** * DOCUMENT ME! * @@ -304,7 +305,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public boolean scrollToPosition(SearchResults results) { - return scrollToPosition(results, true, false); + return scrollToPosition(results, 0, true, false); } /** @@ -317,7 +318,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) { - return scrollToPosition(searchResults, redrawOverview, false); + return scrollToPosition(searchResults, 0, redrawOverview, false); } /** @@ -325,6 +326,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * (if any) * * @param results + * @param verticalOffset + * if greater than zero, allows scrolling to a position below the + * first displayed sequence * @param redrawOverview * - when set, the overview will be recalculated (takes longer) * @param centre @@ -332,6 +336,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, + int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; @@ -390,6 +395,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } } } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + if (!av.getWrapAlignment()) { if ((startv = av.getStartRes()) >= start) @@ -511,47 +522,46 @@ public class AlignmentPanel extends GAlignmentPanel implements */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int height = getAnnotationPanel().adjustPanelHeight(); - - int theight = av.getCharHeight() - * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 - : av.getAlignment().getHiddenSequences().getSize())); - float sscaling = (float) (theight / (1.0 * theight + height)); - float ascaling = (float) (height * 1.0 / alignFrame.getHeight()); - int rheight = alignFrame.getHeight() - height - av.getCharHeight(); + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + if (adjustPanelHeight) { - // NOTE: this logic is different in the applet. Need a better algorithm to - // define behaviour - // try and set height according to alignment - if (ascaling > 0 && sscaling < 0.5) - { - // if the alignment is too big then - // default is 0.5 split - height = alignFrame.getHeight() / 2; - } - else + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate of 75 for menu bar, scale panel, + * hscroll, status bar (as these are not laid out we can't inspect their + * actual heights). Insets gives borders including title bar. + */ + Insets insets = alignFrame.getInsets(); + int availableHeight = alignFrame.getHeight() - 75 - insets.top + - insets.bottom; + + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) { - // if space for more than one sequence row left when annotation is fully - // displayed then set height to annotation height - // otherwise, leave at least two lines of sequence shown. - height = (rheight > av.getCharHeight()) ? height - : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling))); + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); } } else { // maintain same window layout whilst updating sliders - height = annotationScroller.getSize().height; + annotationHeight = annotationScroller.getSize().height; } hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), height)); + .getWidth(), annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), height)); - annotationScroller.validate();// repaint(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); annotationScroller.addNotify(); } @@ -1727,10 +1737,10 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param sr * holds mapped region(s) of this alignment that we are scrolling * 'to'; may be modified for sequence offset by this method - * @param seqOffset + * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResults sr, int seqOffset) + public void scrollToCentre(SearchResults sr, int verticalOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not @@ -1744,7 +1754,6 @@ public class AlignmentPanel extends GAlignmentPanel implements * This is like AlignmentI.findIndex(seq) but here we are matching the * dataset sequence not the aligned sequence */ - int sequenceIndex = 0; boolean matched = false; for (SequenceI seq : seqs) { @@ -1753,20 +1762,16 @@ public class AlignmentPanel extends GAlignmentPanel implements matched = true; break; } - sequenceIndex++; } if (!matched) { return; // failsafe, shouldn't happen } - sequenceIndex = Math.max(0, sequenceIndex - seqOffset); - sr.getResults().get(0) - .setSequence(av.getAlignment().getSequenceAt(sequenceIndex)); /* * Scroll to position but centring the target residue. */ - scrollToPosition(sr, true, true); + scrollToPosition(sr, verticalOffset, true, true); } /** diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 5617bcf..899e8a7 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -2501,14 +2501,14 @@ public abstract class AlignmentViewport implements AlignViewportI, */ protected int findComplementScrollTarget(SearchResults sr) { - final AlignViewportI codingComplement = getCodingComplement(); - if (codingComplement == null || !codingComplement.isFollowHighlight()) + final AlignViewportI complement = getCodingComplement(); + if (complement == null || !complement.isFollowHighlight()) { return 0; } boolean iAmProtein = !getAlignment().isNucleotide(); AlignmentI proteinAlignment = iAmProtein ? getAlignment() - : codingComplement.getAlignment(); + : complement.getAlignment(); if (proteinAlignment == null) { return 0; @@ -2546,7 +2546,7 @@ public abstract class AlignmentViewport implements AlignViewportI, .findMappingsForSequence(sequence, mappings); if (!seqMappings.isEmpty()) { - break; + break; } }