jalview

Clone Tools
  • last updated a few seconds ago
Constraints
Constraints: committers
 
Constraints: files
Constraints: dates
JAL-1994 bugfix in build.xml to prevent proguard from obfuscating dynamically accessed classes used in generating json in jalview. Also added some compile-time dependencies

    • binary
    /appletlib/jsoup-1.8.1.jar
    • binary
    /appletlib/plugin.jar
JAL-1990 added a progress indicator for Structure Chooser interface

    • -19
    • +66
    /src/jalview/gui/StructureChooser.java
    • -1
    • +24
    /src/jalview/jbgui/GStructureChooser.java
merge

JAL-1991 bug fix for some flat-file printers to check for exact modulus in order to avoid outputing an extra redundant header line with empty sequences

JAL-1989 map hidden column ranges

    • -48
    • +133
    /src/jalview/util/MappingUtils.java
    • -0
    • +71
    /test/jalview/util/MappingUtilsTest.java
JAL-1989 more unit tests and encapsulation for ColumnSelection

    • -1
    • +1
    /src/jalview/appletgui/AlignFrame.java
    • -2
    • +13
    /src/jalview/appletgui/ScalePanel.java
    • -2
    • +14
    /src/jalview/appletgui/SeqPanel.java
    • -16
    • +8
    /src/jalview/gui/AnnotationPanel.java
JAL-1544 "more than" not "more that"

    • -1
    • +1
    /help/html/menus/alwannotationpanel.html
merge

JAL-1479 implemented timestamp based caching of SIFTS by providing code which checks if an already downloaded SIFTS file has exceeded a certain threshold upon processing. Also added a method to handle SIFTS entries for cases when an 'entityId' is NOT EQUAL TO 'chainId', this is a heuristic measure achieved using greedy search.

    • -46
    • +175
    /src/jalview/ws/sifts/SiftsClient.java
    • -0
    • +9
    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1982 hotfix to prevent NPE with applet launch on Jpred4 site

    • -1
    • +4
    /src/jalview/appletgui/AlignFrame.java
JAL-1827 code and comment tidy up

    • -36
    • +36
    /src/jalview/ext/jmol/PDBFileWithJmol.java
JAL-1827 refactored to handle missing residues better

    • -205
    • +411
    /src/jalview/ext/jmol/PDBFileWithJmol.java
JAL-1827 added overloaded method for convenience

JAL-1827 reverted text on generic sequence fetcher to not refer to PDB

JAL-1479 refactored DBRef fetching code to StructureChooser to enable applet build

    • -2
    • +3
    /src/jalview/gui/StructureChooser.java
    • -8
    • +0
    /src/jalview/ws/sifts/SiftsClient.java
JAL-1479 applet build debug

    • -0
    • +2
    /src/jalview/gui/StructureChooser.java
    • -19
    • +15
    /src/jalview/ws/sifts/SiftsClient.java
    • -0
    • +12
    /src/jalview/ws/sifts/SiftsSettings.java
JAL-1479 bugfix after decoupling SIFTS preference settings

    • -4
    • +4
    /src/jalview/ws/sifts/SiftsClient.java
JAL-1479 commented out DBRef fetching code from SIFTS to test applet build

    • -7
    • +6
    /src/jalview/ws/sifts/SiftsClient.java
JAL-1479 Refactored Sifts configuration preference in order to rectify applet build

    • -0
    • +16
    /src/jalview/ws/sifts/SiftsSettings.java
JAL-1967 JAL-1479 refactored sequence<->structure mapping implementation

    • -56
    • +66
    /src/jalview/ws/sifts/SiftsClient.java
    • -25
    • +13
    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1479 added transfer of residue annotation for SIFTS mapping, then did some minor house-keeping

    • -8
    • +61
    /src/jalview/ws/sifts/SiftsClient.java
    • -2
    • +2
    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1479 JAL-1957 Added code to enable simultaneous highlight of multiple atoms positions in all chains

    • -7
    • +10
    /src/jalview/ext/jmol/JalviewJmolBinding.java
merge of SIFTs Branch

merge

JAL-1957 JAL-1479 Further optimisation of SIFTs Client and addition of support for multi-chain mapping of uniprot <-> pdb residues

    • -1
    • +7
    /src/jalview/ext/jmol/JmolCommands.java
    • -62
    • +105
    /src/jalview/ws/sifts/SiftsClient.java
    • -1
    • +1
    /test/jalview/ws/sifts/SiftsClientTest.java
JAL 1960 added code to restrict structure chooser to discover only PDB and Uniprot entries when the references are avaiable

    • -26
    • +63
    /src/jalview/gui/StructureChooser.java
JAL-1946 unit tests (and comments) for PID() function

    • -7
    • +25
    /test/jalview/util/ComparisonTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

JAL-1479 SiftClient house keeping

    • -74
    • +188
    /src/jalview/ws/sifts/SiftsClient.java
    • -31
    • +57
    /test/jalview/ws/sifts/SiftsClientTest.java
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/SequenceI.setDBRef to SequenceI.getDBRefs/SequenceI.setDBRefs

    • -1
    • +1
    /src/jalview/datamodel/SequenceGroup.java