From: gmungoc Date: Tue, 28 Jan 2020 12:30:07 +0000 (+0000) Subject: Merge branch 'feature/JAL-3121gffAttributeMap' into develop X-Git-Tag: Release_2_11_1_1~32 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=561472b407c20a9d0a49cd5e87b624e325407751;hp=f89d8403d91ec95d00196bf5f922e2be82ad5c90;p=jalview.git Merge branch 'feature/JAL-3121gffAttributeMap' into develop --- diff --git a/.cvsignore b/.cvsignore deleted file mode 100644 index 51ece2d..0000000 --- a/.cvsignore +++ /dev/null @@ -1,58 +0,0 @@ -NOBACK -Old_bak -bak -classes -das-obert-src -old_lib_signed -temp -tmpextvamsas -.#JalviewX.jpx.1.2 -.#JalviewX.jpx.1.4 -.#JalviewX.jpx.1.7 -.#build.xml.1.23 -.#build.xml.1.24 -.#build.xml.1.25 -.#build.xml.1.27 -1 -FeatureRequests.txt -JalviewApplet.jpx.local -JalviewApplet_jims.jpx -JalviewApplet_jims.jpx.local -JalviewX.jpx.jimpCVS -JalviewX_cvs.jpx -JalviewX_jimsApplet.jpx -JalviewX_jimsApplet.jpx.local -JalviewX_jimsOwn.jpx -JalviewX_jimsOwn.jpx.local -Old.activation.jar -TODO -axis.library -axiskeys -jalview-jim-jalopy.xml -jalview.html -jalview.jpx -jalview.jpx.local -jalviewApplet.jar -jalviewres.library -javah.library -log4j-1.2.8.jar -minimum.library -new.activation.jar -prj.el -regex.library -test.tree -jsrc -keys -Run Jalview Release.launch -Run Jalview Release HugeMem.launch -Run Jalview Groovy Vamsas Release (1).launch -Run Jalview Lite From Jar (1).launch -Run Jalview Groovy Vamsas Release.launch -Run Jalview Lite.launch -Run Jalview Lite From Jar.launch -Run Jalview Questionnaire.launch -Run Jalview Groovy Release.launch -lib-old -statcvs -statcvs_out -jp_gEHhZay.results_files diff --git a/RELEASE b/RELEASE index 1960368..f6e3b96 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ -jalview.release=releases/Release_2_11_Branch -jalview.version=2.11.0 +jalview.release=releases/Release_2_11_1_Branch +jalview.version=2.11.1 diff --git a/dist/.cvsignore b/dist/.cvsignore deleted file mode 100644 index 00a0187..0000000 --- a/dist/.cvsignore +++ /dev/null @@ -1,3 +0,0 @@ -?*.* -*.jar -*.jnlp diff --git a/help/help/html/.cvsignore b/help/help/html/.cvsignore deleted file mode 100644 index 085e8ba..0000000 --- a/help/help/html/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Thumbs.db diff --git a/help/help/html/colourSchemes/.cvsignore b/help/help/html/colourSchemes/.cvsignore deleted file mode 100644 index 085e8ba..0000000 --- a/help/help/html/colourSchemes/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Thumbs.db diff --git a/help/help/html/editing/.cvsignore b/help/help/html/editing/.cvsignore deleted file mode 100644 index 085e8ba..0000000 --- a/help/help/html/editing/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Thumbs.db diff --git a/help/help/html/features/.cvsignore b/help/help/html/features/.cvsignore deleted file mode 100644 index 085e8ba..0000000 --- a/help/help/html/features/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Thumbs.db diff --git a/help/help/html/index.html b/help/help/html/index.html index 62b46a9..36ed33a 100755 --- a/help/help/html/index.html +++ b/help/help/html/index.html @@ -83,9 +83,11 @@
  • Jalview 2 - Java 11 Specific defects - - +
  • + Codon consensus logo incorrectly scaled in gapped + regions of protein alignment. +
    • +
  • + Input Data menu entry is greyed out when PCA View + is restored from a Jalview 2.11 project +
    • +
  • + Alignment panel height can be too small after + 'New View' +
    • +
  • + Display is incorrect after removing gapped + columns within hidden columns +
    • +
  • + Rightmost selection is lost when mouse re-enters + window after dragging left to select columns to left of visible + region +
    • +
  • + Features coloured according to their description + string and thresholded by score in earlier versions of Jalview are + not shown as thresholded features in 2.11. To workaround please + create a Score filter instead. +
    • +
  • + Cancel on Feature Settings dialog doesn't reset group visibility
    • +
  • + F2 doesn't enable/disable keyboard mode in linked CDS/Protein view +
    • +
  • + Closing tree windows with CMD/CTRL-W for + alignments with multiple views can close views unexpectedly +
    • + + Java 11 Specific defects + + diff --git a/help/help/html/webServices/.cvsignore b/help/help/html/webServices/.cvsignore deleted file mode 100644 index 085e8ba..0000000 --- a/help/help/html/webServices/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Thumbs.db diff --git a/resources/.cvsignore b/resources/.cvsignore deleted file mode 100644 index 43d40c0..0000000 --- a/resources/.cvsignore +++ /dev/null @@ -1,2 +0,0 @@ -axisCommons -jalview_mapping.xml diff --git a/resources/images/.cvsignore b/resources/images/.cvsignore deleted file mode 100644 index 1d13d05..0000000 --- a/resources/images/.cvsignore +++ /dev/null @@ -1,10 +0,0 @@ -dna.gif -dna1.gif -dna2.gif -dna3.gif -dna4.gif -dna5.gif -dna6.gif -dna7.gif -dna8.gif -dna9.gif diff --git a/schemas/.cvsignore b/schemas/.cvsignore deleted file mode 100644 index 83ef99a..0000000 --- a/schemas/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -.#jalview.xsd.1.5 \ No newline at end of file diff --git a/src/MCview/.cvsignore b/src/MCview/.cvsignore deleted file mode 100644 index 5ee52a6..0000000 --- a/src/MCview/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -.#PDBViewer.java.1.3 \ No newline at end of file diff --git a/src/jalview/.cvsignore b/src/jalview/.cvsignore deleted file mode 100644 index f436451..0000000 --- a/src/jalview/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -vamsas \ No newline at end of file diff --git a/src/jalview/analysis/.cvsignore b/src/jalview/analysis/.cvsignore deleted file mode 100644 index 33989c8..0000000 --- a/src/jalview/analysis/.cvsignore +++ /dev/null @@ -1,3 +0,0 @@ -.#NJTree.java.1.22 -.#NJTree.java.1.23 -.#SeqsetUtils.java.1.8 diff --git a/src/jalview/datamodel/.cvsignore b/src/jalview/datamodel/.cvsignore deleted file mode 100644 index a4d99ef..0000000 --- a/src/jalview/datamodel/.cvsignore +++ /dev/null @@ -1,5 +0,0 @@ -.#Alignment.java.1.41 -.#Alignment.java.1.42 -.#Alignment.java.1.43 -.#Alignment.java.1.44 -.#AlignmentI.java.1.21 diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 247f5e5..026061b 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1885,15 +1885,6 @@ public class Sequence extends ASequence implements SequenceI List result = getFeatures().findFeatures(startPos, endPos, types); - if (datasetSequence != null) - { - result = datasetSequence.getFeatures().findFeatures(startPos, endPos, - types); - } - else - { - result = sequenceFeatureStore.findFeatures(startPos, endPos, types); - } /* * if end column is gapped, endPos may be to the right, diff --git a/src/jalview/gui/.cvsignore b/src/jalview/gui/.cvsignore deleted file mode 100644 index a1659ce..0000000 --- a/src/jalview/gui/.cvsignore +++ /dev/null @@ -1,11 +0,0 @@ -.#AlignViewport.java.1.62 -.#AlignViewport.java.1.63 -.#AnnotationPanel.java.1.57 -.#FeatureRenderer.java.1.22 -.#OverviewPanel.java.1.26 -.#Preferences.java.1.26 -.#Preferences.java.1.28 -.#Preferences.java.1.29 -.#SequenceFetcher.java.1.23 -.#SequenceFetcher.java.1.24 -.#TreePanel.java.1.33 diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 441dca7..11d5e39 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -282,7 +282,8 @@ public class FeatureSettings extends JPanel @Override public void mousePressed(MouseEvent evt) { - selectedRow = table.rowAtPoint(evt.getPoint()); + Point pt = evt.getPoint(); + selectedRow = table.rowAtPoint(pt); String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN); if (evt.isPopupTrigger()) { @@ -290,7 +291,8 @@ public class FeatureSettings extends JPanel popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(), evt.getY()); } - else if (evt.getClickCount() == 2) + else if (evt.getClickCount() == 2 + && table.columnAtPoint(pt) == TYPE_COLUMN) { boolean invertSelection = evt.isAltDown(); boolean toggleSelection = Platform.isControlDown(evt); diff --git a/src/jalview/io/.cvsignore b/src/jalview/io/.cvsignore deleted file mode 100644 index 485d807..0000000 --- a/src/jalview/io/.cvsignore +++ /dev/null @@ -1,2 +0,0 @@ -.#DasSequenceFeatureFetcher.java.1.17 -cli diff --git a/src/jalview/jbgui/.cvsignore b/src/jalview/jbgui/.cvsignore deleted file mode 100644 index 1cb80c3..0000000 --- a/src/jalview/jbgui/.cvsignore +++ /dev/null @@ -1,3 +0,0 @@ -#GPreferences.java# -.#GPreferences.java.1.20 -.#GPreferences.java.1.22 diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 9f98ffa..1b4a8bd 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -2487,7 +2487,7 @@ public class GPreferences extends JPanel { try { - i = Integer.parseInt((String) s.getValue()); + i = ((Integer) s.getValue()).intValue(); } catch (Exception e) { Cache.log.error( @@ -2506,6 +2506,10 @@ public class GPreferences extends JPanel { max = def; } + if (def < min) + { + def = min; + } SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1); s.setModel(sModel); diff --git a/src/jalview/util/.cvsignore b/src/jalview/util/.cvsignore deleted file mode 100644 index c5b8965..0000000 --- a/src/jalview/util/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -InstanceDiscoverer.java \ No newline at end of file diff --git a/src/jalview/ws/.cvsignore b/src/jalview/ws/.cvsignore deleted file mode 100644 index be25ffb..0000000 --- a/src/jalview/ws/.cvsignore +++ /dev/null @@ -1,3 +0,0 @@ -.#JPredClient.java.1.25 -.#JPredClient.java.1.31 -.#MsaWSClient.java.1.26 diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 81ec443..a262147 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -410,7 +410,7 @@ public class CrossRefTest * Test for finding 'product' sequences for the case where the selected * sequence has a dbref with no mapping, triggering a fetch from database */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_withFetch() { SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); @@ -464,7 +464,7 @@ public class CrossRefTest * Test for finding 'product' sequences for the case where both gene and * transcript sequences have dbrefs to Uniprot. */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_forGeneAndTranscripts() { /* @@ -561,7 +561,7 @@ public class CrossRefTest * - X06707 dbrefs to P0CE19/20 mapped to original Uniprot sequences * */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_uniprotEmblManyToMany() { /* diff --git a/utils/.cvsignore b/utils/.cvsignore deleted file mode 100644 index 823caeb..0000000 --- a/utils/.cvsignore +++ /dev/null @@ -1,2 +0,0 @@ -help2Website.class -getJavaVersion.class diff --git a/utils/InstallAnywhere/.cvsignore b/utils/InstallAnywhere/.cvsignore deleted file mode 100644 index a44ca6b..0000000 --- a/utils/InstallAnywhere/.cvsignore +++ /dev/null @@ -1 +0,0 @@ -Jalview_modified.iap_xml