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[Bioclipse-commit] [bioclipse/bioclipse.ds] d906fa: implemented sign height and corrected resource>par...

From: <noreply@gi...> - 2011-03-07 04:02

Branch: refs/heads/sdk
Home:   https://github.com/bioclipse/bioclipse.ds

Commit: d906fa7c44badbfca47b6934de31427c9151ca9f
    https://github.com/bioclipse/bioclipse.ds/commit/d906fa7c44badbfca47b6934de31427c9151ca9f
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/pdewizard/DSTemplate.java

Log Message:
-----------
implemented sign height and corrected resource>param


Commit: 6ad9a705a2ef3086ce286a77a7cd98548cbade05
    https://github.com/bioclipse/bioclipse.ds/commit/6ad9a705a2ef3086ce286a77a7cd98548cbade05
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/QSARbuilder.java

Log Message:
-----------
Added getters/setters in QSARbuilder


Commit: b93d250b79842fb87f708b0c17765cf15e8af2f3
    https://github.com/bioclipse/bioclipse.ds/commit/b93d250b79842fb87f708b0c17765cf15e8af2f3
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M features/net.bioclipse.ds_feature/feature.xml
  M plugins/net.bioclipse.ds.libsvm/.classpath
  M plugins/net.bioclipse.ds.libsvm/META-INF/MANIFEST.MF
  A plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMPrediction.java
  M plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMTest.java
  M plugins/net.bioclipse.ds.signatures/META-INF/MANIFEST.MF

Log Message:
-----------
Rewrote libsvm-sign impl for 3.0 and sparse repr.


Commit: 1867d7ed491aea1efff51a1f210c9d170c742b7f
    https://github.com/bioclipse/bioclipse.ds/commit/1867d7ed491aea1efff51a1f210c9d170c742b7f
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/pdewizard/DSTemplate.java

Log Message:
-----------
Updated for sparse repr class


Commit: 44ffd53e911e2e7c4c84ed84238763b2c91e9866
    https://github.com/bioclipse/bioclipse.ds/commit/44ffd53e911e2e7c4c84ed84238763b2c91e9866
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  A plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMBase.java
  M plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMPrediction.java
  R plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMTest.java

Log Message:
-----------
Renamed classes for clarity and fixed init in regression as well as classification


Commit: 8f4ea961a7ea8a0c019a49fa9ac937c3010234d9
    https://github.com/bioclipse/bioclipse.ds/commit/8f4ea961a7ea8a0c019a49fa9ac937c3010234d9
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  R plugins/net.bioclipse.ds.ames/models/ames.model
  R plugins/net.bioclipse.ds.ames/models/ames.range
  R plugins/net.bioclipse.ds.ames/models/ames.signatures

Log Message:
-----------
Removed deprecated models


Commit: 88a0e7094dc909767f01ee5bf0fc473314fab2ec
    https://github.com/bioclipse/bioclipse.ds/commit/88a0e7094dc909767f01ee5bf0fc473314fab2ec
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.ames/plugin.xml

Log Message:
-----------
Added parameters required for sparse impl


Commit: 402f9cd5d02fc02f5f1d4867920d3355191a0802
    https://github.com/bioclipse/bioclipse.ds/commit/402f9cd5d02fc02f5f1d4867920d3355191a0802
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M features/net.bioclipse.ds_feature/feature.xml

Log Message:
-----------
Removed AHR and CPDB since need to build sparse models for them


Compare: https://github.com/bioclipse/bioclipse.ds/compare/3e1c50f...402f9cd

[Bioclipse-commit] [bioclipse/bioclipse.ds] 9afa97: replaced with libsvm 3.0

From: <noreply@gi...> - 2011-03-07 01:53

Branch: refs/heads/sdk
Home:   https://github.com/bioclipse/bioclipse.ds

Commit: 9afa978861341c57e5ab4f7bb64de48192ae3560
    https://github.com/bioclipse/bioclipse.ds/commit/9afa978861341c57e5ab4f7bb64de48192ae3560
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  R plugins/net.bioclipse.ds.sdk/lib/libsvm.jar
  M plugins/net.bioclipse.libsvm/lib/libsvm.jar

Log Message:
-----------
replaced with libsvm 3.0


Commit: 379f049a31f5fb8fe66f3431f042980368285daa
    https://github.com/bioclipse/bioclipse.ds/commit/379f049a31f5fb8fe66f3431f042980368285daa
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/cdk/CDKHelper.java
  A plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/libsvm/SignPredict.java
  A plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/libsvm/SignTest.java
  R plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/SignPredict.java
  R plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/SignTest.java
  R plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/SignTools.java

Log Message:
-----------
refactored libsvm test classes


Commit: 1df6ead8924b5845f8db9c478c01eea30542cd35
    https://github.com/bioclipse/bioclipse.ds/commit/1df6ead8924b5845f8db9c478c01eea30542cd35
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  A plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/ConsoleProgressMonitor.java
  A plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/qsar/QSARbuilder.java

Log Message:
-----------
Implemented QSARBuilder


Commit: af6a149e6dc479929ba5035635ad9358443757f5
    https://github.com/bioclipse/bioclipse.ds/commit/af6a149e6dc479929ba5035635ad9358443757f5
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  A plugins/net.bioclipse.ds.ames/models/ames.model2
  A plugins/net.bioclipse.ds.ames/models/ames.signatures2

Log Message:
-----------
New models for ames


Commit: 91c30a7042a37e5bef1d079b0d3632bb417901f1
    https://github.com/bioclipse/bioclipse.ds/commit/91c30a7042a37e5bef1d079b0d3632bb417901f1
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.libsvm/META-INF/MANIFEST.MF

Log Message:
-----------
We are now at libsvm v 3.0


Commit: 1509d8d7a2bca2da4b20cfd3511813c3038eb3c4
    https://github.com/bioclipse/bioclipse.ds/commit/1509d8d7a2bca2da4b20cfd3511813c3038eb3c4
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/.classpath
  M plugins/net.bioclipse.ds.sdk/META-INF/MANIFEST.MF
  M plugins/net.bioclipse.ds.sdk/build.properties

Log Message:
-----------
Clean up manifest after libsvm refactoring


Commit: ad3f3ebb28db7bd54d8e465d748b6acd5cd2181f
    https://github.com/bioclipse/bioclipse.ds/commit/ad3f3ebb28db7bd54d8e465d748b6acd5cd2181f
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  R plugins/net.bioclipse.libsvm/src/net/bioclipse/libsvm/Activator.java

Log Message:
-----------
removed unused activator


Commit: 3e1c50f076ae968a70113de0c18af4b651e0ce95
    https://github.com/bioclipse/bioclipse.ds/commit/3e1c50f076ae968a70113de0c18af4b651e0ce95
Author: Ola Spjuth <ola.spjuth@...>
Date:   2011-03-06 (Sun, 06 Mar 2011)

Changed paths:
  M plugins/net.bioclipse.ds.sdk/src/net/bioclipse/ds/sdk/pdewizard/DSTemplate.java

Log Message:
-----------
implemented files and extensions for QSAR


Compare: https://github.com/bioclipse/bioclipse.ds/compare/731c1ad...3e1c50f