From: gmungoc Date: Wed, 9 Aug 2017 10:45:53 +0000 (+0100) Subject: Merge branch 'develop' into features/JAL-2446NCList X-Git-Tag: Release_2_10_3b1~156 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f8feecc3dcaa6546effb25f2bc0362779fc7c1a;hp=3c6289e26f1060fd072f0eb8820cc206687b000f;p=jalview.git Merge branch 'develop' into features/JAL-2446NCList --- diff --git a/help/html/features/overview.html b/help/html/features/overview.html index 4f26592..ac5aecb 100755 --- a/help/html/features/overview.html +++ b/help/html/features/overview.html @@ -31,11 +31,20 @@

The red box indicates the currently viewed region of the alignment, this may be moved by clicking and dragging with the mouse.

-

Right-click (or CMD-Click) to open the - overview's popup menu. This provides an option to include hidden - regions in the overview (shown as dark-grey rows and columns).

- The option to include/exclude hidden regions in the - overview was introduced in Jalview 2.10.2. +

Click anywhere else in the overview to centre the view on that + position

+

+

+ Hiding hidden regions in the overview +

+

+ Hidden sequences and columns are by default shown as dark-grey rows + and columns in the overview. Hidden regions can also be omitted + entirely (to make the Overview 'WYSIWIG') by Right-clicking + (or CMD-Clicking) to open the overview's popup menu.
+
The option to include/exclude hidden regions in the + overview was introduced in Jalview 2.10.2. +

diff --git a/help/html/releases.html b/help/html/releases.html index ea9bbf5..3482f71 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -107,17 +107,29 @@ li:before { Custom shading schemes created via groovy scripts -
  • - linked scrolling of CDS/Protein views - via Overview or sequence motif search operations -
    • -
  • - Efficiency improvements for interacting - with alignment and overview windows -
    • -
  • - Hidden columns and sequences can be - omitted in Overview +
  • Improved overview window +
  • Posterior probability annotation from @@ -570,6 +582,8 @@ li:before { due to 'null' string rather than empty string used for residues with no corresponding PDB mapping).
    • +
  • User defined colourschemes called 'User Defined' don't appear in Colours menu
    • +
  • diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 4147177..d679217 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -643,7 +643,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public void setWrapAlignment(boolean wrap) { - vpRanges.setStartSeq(0); + vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight()); vpRanges.setStartRes(0); scalePanelHolder.setVisible(!wrap); diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 39b718d..417bb06 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -634,7 +634,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, public void fastPaint(int horizontal) { - if (horizontal == 0 + if (horizontal == 0 || gg == null || av.getAlignment().getAlignmentAnnotation() == null || av.getAlignment().getAlignmentAnnotation().length < 1) { diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 162d100..8a59a4b 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -3324,7 +3324,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 'User Defined' opens a panel to configure or load a * user-defined colour scheme */ - if (ResidueColourScheme.USER_DEFINED.equals(name)) + if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) { new UserDefinedColours(alignPanel); return; diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java index b2b9574..8ffc070 100644 --- a/src/jalview/gui/ColourMenuHelper.java +++ b/src/jalview/gui/ColourMenuHelper.java @@ -177,13 +177,13 @@ public class ColourMenuHelper final String label = MessageManager.getString("action.user_defined"); JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem( label); - userDefinedColour.setName(ResidueColourScheme.USER_DEFINED); + userDefinedColour.setName(ResidueColourScheme.USER_DEFINED_MENU); userDefinedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED); + client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED_MENU); } }); colourMenu.add(userDefinedColour); @@ -230,7 +230,7 @@ public class ColourMenuHelper { none = radioButton; } - if (ResidueColourScheme.USER_DEFINED.equals(buttonName)) + if (ResidueColourScheme.USER_DEFINED_MENU.equals(buttonName)) { userDefined = radioButton; } diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java index b47b82e..6aa798e 100755 --- a/src/jalview/schemes/ResidueColourScheme.java +++ b/src/jalview/schemes/ResidueColourScheme.java @@ -35,9 +35,17 @@ public abstract class ResidueColourScheme implements ColourSchemeI { public static final String NONE = "None"; + /* + * default display name for a user defined colour scheme + */ public static final String USER_DEFINED = "User Defined"; /* + * name for (new) "User Defined.." colour scheme menu item + */ + public static final String USER_DEFINED_MENU = "*User Defined*"; + + /* * lookup up by character value e.g. 'G' to the colors array index * e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K */ diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java index 8e58c20..256862d 100755 --- a/src/jalview/schemes/UserColourScheme.java +++ b/src/jalview/schemes/UserColourScheme.java @@ -273,7 +273,7 @@ public class UserColourScheme extends ResidueColourScheme { return schemeName; } - return "User Defined"; + return ResidueColourScheme.USER_DEFINED; } /**