Added README and reorganized directory structure (breaks code)
authorW. Trevor King <wking@drexel.edu>
Thu, 17 Dec 2009 19:19:40 +0000 (14:19 -0500)
committerW. Trevor King <wking@drexel.edu>
Thu, 17 Dec 2009 19:19:40 +0000 (14:19 -0500)
38 files changed:
README [new file with mode: 0644]
conf/convfilt.conf [moved from convfilt.conf with 100% similarity]
conf/hooke.conf [moved from hooke.conf with 100% similarity]
conf/pca_config.txt [moved from pca_config.txt with 100% similarity]
doc/hooke.jpg [moved from hooke.jpg with 100% similarity]
hooke/driver/csvdriver.py [moved from csvdriver.py with 100% similarity]
hooke/driver/hemingclamp.py [moved from hemingclamp.py with 100% similarity]
hooke/driver/jpk.py [moved from jpk.py with 100% similarity]
hooke/driver/mcs.py [moved from mcs.py with 100% similarity]
hooke/driver/mfp1dexport.py [moved from mfp1dexport.py with 100% similarity]
hooke/driver/picoforce.py [moved from picoforce.py with 100% similarity]
hooke/driver/picoforcealt.py [moved from picoforcealt.py with 100% similarity]
hooke/driver/tutorialdriver.py [moved from tutorialdriver.py with 100% similarity]
hooke/hooke.py [moved from hooke.py with 100% similarity]
hooke/hooke_cli.py [moved from hooke_cli.py with 100% similarity]
hooke/libhooke.py [moved from libhooke.py with 100% similarity]
hooke/libhookecurve.py [moved from libhookecurve.py with 100% similarity]
hooke/libinput.py [moved from libinput.py with 100% similarity]
hooke/liboutlet.py [moved from liboutlet.py with 100% similarity]
hooke/libpeakspot.py [moved from libpeakspot.py with 100% similarity]
hooke/libviewer.py [moved from libviewer.py with 100% similarity]
hooke/plugin/autopeak.py [moved from autopeak.py with 100% similarity]
hooke/plugin/cut.py [moved from cut.py with 100% similarity]
hooke/plugin/fit.py [moved from fit.py with 100% similarity]
hooke/plugin/flatfilts.py [moved from flatfilts.py with 100% similarity]
hooke/plugin/generalclamp.py [moved from generalclamp.py with 100% similarity]
hooke/plugin/generaltccd.py [moved from generaltccd.py with 100% similarity]
hooke/plugin/generalvclamp.py [moved from generalvclamp.py with 100% similarity]
hooke/plugin/macro.py [moved from macro.py with 100% similarity]
hooke/plugin/massanalysis.py [moved from massanalysis.py with 100% similarity]
hooke/plugin/multidistance.py [moved from multidistance.py with 100% similarity]
hooke/plugin/pcluster.py [moved from pcluster.py with 100% similarity]
hooke/plugin/procplots.py [moved from procplots.py with 100% similarity]
hooke/plugin/superimpose.py [moved from superimpose.py with 100% similarity]
hooke/plugin/tutorial.py [moved from tutorial.py with 100% similarity]
hooke/plugin/viewer.py [moved from viewer.py with 100% similarity]
hooke/test/default.000 [moved from default.000 with 100% similarity]
hooke/test/test.hkp [moved from test.hkp with 100% similarity]

diff --git a/README b/README
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+What is it?
+===========
+
+It is a software for the (semiautomatic) analysis and filtering of
+force curves. Force curves are the output of an analytical technique
+called force spectroscopy. A force spectroscopy experiment usually
+requires the analysis of thousands of force curves at a time. As of
+today, there is no standard, free software for the analysis of force
+curves. Hooke aims to solve that.
+
+What it does?
+=============
+
+  * View, annotate, measure force curves
+  * Worm-like chain and freely-jointed chain fit of force peaks
+  * Automatic convolution-based filtering of empty curves
+  * Automatic fit and measurement of multiple force peaks
+  * Handles force-clamp force experiments (experimental)
+  * It is extensible by users by mean of plugins and drivers
+
+See the Google Code website for more details
+  http://code.google.com/p/hooke/
+
+Is this published in some peer-reviewed journal?
+================================================
+
+Sandal M, Benedetti F, Brucale M, Gomez-Casado A, Samorì B.
+"Hooke: an open software platform for force spectroscopy."
+Bioinformatics, 2009 25(11):1428-1430.
+doi:10.1093/bioinformatics/btp180
+
+Please cite Hooke if you use it.
+
+Troubleshooting
+===============
+
+If you have troubles in using it, before throwing it in the trash:
+  1) try look at the TroubleShooting page or in the discussion group
+  2) ask a question in the discussion group!
+http://groups.google.com/group/hookesoftware
+
+Disclaimer
+==========
+
+Remember that Hooke is still experimental software! It has been mostly
+done to fit the needs of its authors, and there is no guarantee it
+will do what you need. However, you can write us/help us improve it so
+that it does. We aim to make of Hooke a little, universal tool that
+can help your research.
similarity index 100%
rename from convfilt.conf
rename to conf/convfilt.conf
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rename from hooke.conf
rename to conf/hooke.conf
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rename from pca_config.txt
rename to conf/pca_config.txt
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rename from hooke.jpg
rename to doc/hooke.jpg
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rename from csvdriver.py
rename to hooke/driver/csvdriver.py
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rename from hemingclamp.py
rename to hooke/driver/hemingclamp.py
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rename from jpk.py
rename to hooke/driver/jpk.py
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rename from mcs.py
rename to hooke/driver/mcs.py
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rename from mfp1dexport.py
rename to hooke/driver/mfp1dexport.py
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rename from picoforce.py
rename to hooke/driver/picoforce.py
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rename from picoforcealt.py
rename to hooke/driver/picoforcealt.py
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rename from hooke.py
rename to hooke/hooke.py
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rename from hooke_cli.py
rename to hooke/hooke_cli.py
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rename from libhooke.py
rename to hooke/libhooke.py
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rename from libhookecurve.py
rename to hooke/libhookecurve.py
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rename from libinput.py
rename to hooke/libinput.py
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rename from liboutlet.py
rename to hooke/liboutlet.py
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rename from libpeakspot.py
rename to hooke/libpeakspot.py
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rename from libviewer.py
rename to hooke/libviewer.py
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rename from autopeak.py
rename to hooke/plugin/autopeak.py
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rename from cut.py
rename to hooke/plugin/cut.py
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rename from fit.py
rename to hooke/plugin/fit.py
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rename from flatfilts.py
rename to hooke/plugin/flatfilts.py
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rename from generalclamp.py
rename to hooke/plugin/generalclamp.py
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rename from generaltccd.py
rename to hooke/plugin/generaltccd.py
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rename from macro.py
rename to hooke/plugin/macro.py
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rename from massanalysis.py
rename to hooke/plugin/massanalysis.py
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rename from pcluster.py
rename to hooke/plugin/pcluster.py
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rename from procplots.py
rename to hooke/plugin/procplots.py
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rename from superimpose.py
rename to hooke/plugin/superimpose.py
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rename from tutorial.py
rename to hooke/plugin/tutorial.py
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rename from viewer.py
rename to hooke/plugin/viewer.py
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rename from default.000
rename to hooke/test/default.000
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rename from test.hkp
rename to hooke/test/test.hkp