X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=a677401bf41bb39eacca1c96fe70a946ada4dc5b;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=5a2c5ef4d5d2bf9101b6c380c57918e49aef53d9;hpb=ed2283c5f54da377a2a2fdbdb7aec75ed7041714;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 5a2c5ef..a677401 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,15 @@ */ package jalview.appletgui; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.JalviewLite; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceI; +import jalview.structure.StructureSelectionManager; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; @@ -34,15 +43,6 @@ import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; import java.util.List; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.JalviewLite; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; -import jalview.datamodel.SequenceI; -import jalview.structure.StructureSelectionManager; - public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel { @@ -162,15 +162,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { return av; } + public SequenceRenderer getSequenceRenderer() { return seqPanel.seqCanvas.sr; } + @Override public jalview.api.FeatureRenderer getFeatureRenderer() { return seqPanel.seqCanvas.fr; } + @Override public jalview.api.FeatureRenderer cloneFeatureRenderer() { @@ -178,6 +181,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, nfr.transferSettings(seqPanel.seqCanvas.fr); return nfr; } + public void alignmentChanged() { av.alignmentChanged(this); @@ -449,37 +453,37 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // setScrollValues(start, seqIndex); // } // logic copied from jalview.gui.AlignmentPanel: - if ((startv = av.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - setScrollValues(start - 1, seqIndex); - } - else if ((endv = av.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - setScrollValues(startv + 1 + end - endv, seqIndex); - } - else if ((starts = av.getStartSeq()) > seqIndex) - { - /* - * Scroll up to make start of search results visible - */ - setScrollValues(av.getStartRes(), seqIndex); - } - else if ((ends = av.getEndSeq()) <= seqIndex) - { - /* - * Scroll down to make end of search results visible - */ - setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); - } + if ((startv = av.getStartRes()) >= start) + { /* - * Else results are already visible - no need to scroll + * Scroll left to make start of search results visible */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(av.getStartRes(), seqIndex); + } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } + /* + * Else results are already visible - no need to scroll + */ } else { @@ -552,70 +556,60 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } /** - * calculate the annotation dimensions and refresh slider values accordingly. - * need to do repaints/notifys afterwards. + * Calculate the annotation dimensions and refresh slider values accordingly. + * Need to do repaints/notifys afterwards. */ protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - boolean modified = false; - int height = av.calcPanelHeight(); - int minsize = 0; - if (hscroll.isVisible()) - { - height += (minsize = hscroll.getPreferredSize().height); - } - if (apvscroll.isVisible()) - { - minsize += apvscroll.getPreferredSize().height; - } - int mheight = height; - Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize(); - int seqandannot = d.height - scalePanelHolder.getSize().height; + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + int annotationHeight = av.calcPanelHeight(); + + int mheight = annotationHeight; + Dimension d = sequenceHolderPanel.getSize(); + + int availableHeight = d.height - scalePanelHolder.getHeight(); if (adjustPanelHeight) { - // NOTE: this logic is different in the application. Need a better - // algorithm to define behaviour - // sets initial preferred height - // try and set height according to alignment - float sscaling = (float) ((av.getCharHeight() * av.getAlignment() - .getHeight()) / (1.0 * mheight)); - if (sscaling > 0.5) - { - // if the alignment is too big then - // default is 0.5 split - height = seqandannot / 2; - } - else + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) { - // otherwise just set the panel so that one row of sequence is visible - height = -av.getCharHeight() * 1 - + (int) (seqandannot * (1 - sscaling)); + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); } } else { // maintain same window layout whilst updating sliders - height = annotationPanelHolder.getSize().height; + annotationHeight = annotationPanelHolder.getSize().height; } - if (seqandannot - height < 5) + if (availableHeight - annotationHeight < 5) { - height = seqandannot; + annotationHeight = availableHeight; } - annotationPanel.setSize(new Dimension(d.width, height)); - alabels.setSize(new Dimension(e.width, height)); - annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); - annotationPanelHolder.setSize(new Dimension(d.width, height)); + + annotationPanel.setSize(new Dimension(d.width, annotationHeight)); + annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight)); // seqPanelHolder.setSize(d.width, seqandannot - height); seqPanel.seqCanvas .setSize(d.width, seqPanel.seqCanvas.getSize().height); + + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setSize(new Dimension(e.width, + annotationHeight)); + int s = apvscroll.getValue(); - if (s > mheight - height) + if (s > mheight - annotationHeight) { s = 0; } - apvscroll.setValues(s, height, 0, mheight); + apvscroll.setValues(s, annotationHeight, 0, mheight); annotationPanel.setScrollOffset(apvscroll.getValue(), false); alabels.setScrollOffset(apvscroll.getValue(), false); } @@ -963,6 +957,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, if (updateOverview) { + // TODO: determine if this paintAlignment changed structure colours jalview.structure.StructureSelectionManager .getStructureSelectionManager(av.applet) .sequenceColoursChanged(this); @@ -983,7 +978,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { invalidate(); Dimension d = idPanel.idCanvas.getSize(); - idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); + final int canvasHeight = seqPanel.seqCanvas.getSize().height; + if (canvasHeight != d.height) + { + idPanel.idCanvas.setSize(d.width, canvasHeight); + } if (av.getWrapAlignment()) {