From: cmzmasek@gmail.com Date: Sat, 29 Dec 2012 20:32:33 +0000 (+0000) Subject: moved to: https://sites.google.com/site/cmzmasek/home/software/forester X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git moved to: https://sites.google.com/site/cmzmasek/home/software/forester --- diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java index 5a6a32a..9f18f81 100644 --- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java +++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.analysis; diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInferenceException.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInferenceException.java index dd65918..bb4bca0 100644 --- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInferenceException.java +++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInferenceException.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.analysis; diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index 2bc654f..48b434c 100644 --- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java +++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.analysis; diff --git a/forester/java/src/org/forester/application/confadd.java b/forester/java/src/org/forester/application/confadd.java index 3fed60c..b48cde9 100644 --- a/forester/java/src/org/forester/application/confadd.java +++ b/forester/java/src/org/forester/application/confadd.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/count_support.java b/forester/java/src/org/forester/application/count_support.java index 3096e21..b57f3c5 100644 --- a/forester/java/src/org/forester/application/count_support.java +++ b/forester/java/src/org/forester/application/count_support.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java index 8084ee2..ba79613 100644 --- a/forester/java/src/org/forester/application/decorator.java +++ b/forester/java/src/org/forester/application/decorator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/gene_tree_preprocess.java b/forester/java/src/org/forester/application/gene_tree_preprocess.java index bcb93f4..06f2803 100644 --- a/forester/java/src/org/forester/application/gene_tree_preprocess.java +++ b/forester/java/src/org/forester/application/gene_tree_preprocess.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/goac.java b/forester/java/src/org/forester/application/goac.java index a753694..37b9d12 100644 --- a/forester/java/src/org/forester/application/goac.java +++ b/forester/java/src/org/forester/application/goac.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java index 295e542..9e3f326 100644 --- a/forester/java/src/org/forester/application/gsdi.java +++ b/forester/java/src/org/forester/application/gsdi.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/mcc.java b/forester/java/src/org/forester/application/mcc.java index 70b520f..23320fc 100644 --- a/forester/java/src/org/forester/application/mcc.java +++ b/forester/java/src/org/forester/application/mcc.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/nhx_too.java b/forester/java/src/org/forester/application/nhx_too.java index 1d212f0..1061c5c 100644 --- a/forester/java/src/org/forester/application/nhx_too.java +++ b/forester/java/src/org/forester/application/nhx_too.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/nj.java b/forester/java/src/org/forester/application/nj.java index 6bce553..0f1ef3e 100644 --- a/forester/java/src/org/forester/application/nj.java +++ b/forester/java/src/org/forester/application/nj.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/obo_tool.java b/forester/java/src/org/forester/application/obo_tool.java index 17281b7..abd1cba 100644 --- a/forester/java/src/org/forester/application/obo_tool.java +++ b/forester/java/src/org/forester/application/obo_tool.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/pccx.java b/forester/java/src/org/forester/application/pccx.java index 44839c9..48ca75a 100644 --- a/forester/java/src/org/forester/application/pccx.java +++ b/forester/java/src/org/forester/application/pccx.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/pfam2go_extractor.java b/forester/java/src/org/forester/application/pfam2go_extractor.java index edf1940..d9f4cd3 100644 --- a/forester/java/src/org/forester/application/pfam2go_extractor.java +++ b/forester/java/src/org/forester/application/pfam2go_extractor.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/pfam_go.java b/forester/java/src/org/forester/application/pfam_go.java index 75f0381..475b5d4 100644 --- a/forester/java/src/org/forester/application/pfam_go.java +++ b/forester/java/src/org/forester/application/pfam_go.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/pfamacc2go.java b/forester/java/src/org/forester/application/pfamacc2go.java index 69793ef..ce34dc7 100644 --- a/forester/java/src/org/forester/application/pfamacc2go.java +++ b/forester/java/src/org/forester/application/pfamacc2go.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/pfamacc2pfamid.java b/forester/java/src/org/forester/application/pfamacc2pfamid.java index 24da6d0..0abafb5 100644 --- a/forester/java/src/org/forester/application/pfamacc2pfamid.java +++ b/forester/java/src/org/forester/application/pfamacc2pfamid.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/phyloxml_converter.java b/forester/java/src/org/forester/application/phyloxml_converter.java index 24fe964..f82779c 100644 --- a/forester/java/src/org/forester/application/phyloxml_converter.java +++ b/forester/java/src/org/forester/application/phyloxml_converter.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java index 1e8745f..a1cc0c0 100644 --- a/forester/java/src/org/forester/application/rio.java +++ b/forester/java/src/org/forester/application/rio.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/strip.java b/forester/java/src/org/forester/application/strip.java index f374154..14aa69e 100644 --- a/forester/java/src/org/forester/application/strip.java +++ b/forester/java/src/org/forester/application/strip.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/support_statistics.java b/forester/java/src/org/forester/application/support_statistics.java index a6b6c03..ae8083a 100644 --- a/forester/java/src/org/forester/application/support_statistics.java +++ b/forester/java/src/org/forester/application/support_statistics.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/support_transfer.java b/forester/java/src/org/forester/application/support_transfer.java index 3f1af34..59090c2 100644 --- a/forester/java/src/org/forester/application/support_transfer.java +++ b/forester/java/src/org/forester/application/support_transfer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 2218f40..5bc8173 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.application; diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 97e8304..c2dfc54 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java index 88c9588..546a8c0 100644 --- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java +++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java index 837a24b..b209dbc 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxA.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java b/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java index 2866b14..59ec4b2 100644 --- a/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java +++ b/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index deaaec8..679ec85 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 5558a84..4dc637d 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -49,7 +49,7 @@ public final class Constants { "Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; final static boolean VERBOSE_DEFAULT = false; final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 200; - final static String AUTHOR_EMAIL = "phylosoft@gmail.com"; + final static String AUTHOR_EMAIL = "phyloxml@gmail.com"; final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = 0; final static float BUTTON_ZOOM_IN_FACTOR = 1.25f; final static float BUTTON_ZOOM_OUT_FACTOR = 1 / Constants.BUTTON_ZOOM_IN_FACTOR; @@ -74,7 +74,7 @@ public final class Constants { static final int A4_SIZE_X = 595; static final int A4_SIZE_Y = 845; final static float PDF_LINE_WIDTH_DEFAULT = 0.5f; - final static String APTX_WEB_SITE = "http://www.phylosoft.org/archaeopteryx/"; + final static String APTX_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"; final static String PHYLOXML_WEB_SITE = ForesterConstants.PHYLO_XML_LOCATION; final static String PHYLOXML_REFERENCE_URL = "http://www.biomedcentral.com/1471-2105/10/356/"; final static String APTX_REFERENCE_URL = "http://www.biomedcentral.com/bmcbioinformatics/"; diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index e25ef2c..12bdf3f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/FontChooser.java b/forester/java/src/org/forester/archaeopteryx/FontChooser.java index bf900af..694a6ee 100644 --- a/forester/java/src/org/forester/archaeopteryx/FontChooser.java +++ b/forester/java/src/org/forester/archaeopteryx/FontChooser.java @@ -9,7 +9,7 @@ // by: James Bardsley (torasin@torasin.com) // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index 72f2e27..c3da73b 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index fc8a103..2bf378a 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index d3b700d..ca14a87 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanel.java b/forester/java/src/org/forester/archaeopteryx/MainPanel.java index 62b7d00..885e378 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/MainPanel.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java b/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java index 4d4d684..80a96c0 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java +++ b/forester/java/src/org/forester/archaeopteryx/MainPanelApplets.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/MouseListener.java b/forester/java/src/org/forester/archaeopteryx/MouseListener.java index eb6e64f..8239a48 100644 --- a/forester/java/src/org/forester/archaeopteryx/MouseListener.java +++ b/forester/java/src/org/forester/archaeopteryx/MouseListener.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java index 2392620..1892411 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodeEditPanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/ +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/NodeFrame.java b/forester/java/src/org/forester/archaeopteryx/NodeFrame.java index 2b37494..e929451 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodeFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/NodeFrame.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java index 00a09d7..686b348 100644 --- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/ +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index cb067ab..43b8fec 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java index b1c7feb..6305a85 100644 --- a/forester/java/src/org/forester/archaeopteryx/PdfExporter.java +++ b/forester/java/src/org/forester/archaeopteryx/PdfExporter.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/Printer.java b/forester/java/src/org/forester/archaeopteryx/Printer.java index bca603e..ff00be5 100644 --- a/forester/java/src/org/forester/archaeopteryx/Printer.java +++ b/forester/java/src/org/forester/archaeopteryx/Printer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/TextFrame.java b/forester/java/src/org/forester/archaeopteryx/TextFrame.java index 55c12d4..11954fa 100644 --- a/forester/java/src/org/forester/archaeopteryx/TextFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/TextFrame.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java index 9881efa..7e11577 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeColorSet.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java index 29ae89c..80c7bd2 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java +++ b/forester/java/src/org/forester/archaeopteryx/TreeFontSet.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 8bc57e2..6b26c29 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java index 432c2ac..ea4bca0 100644 --- a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java +++ b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/WebLink.java b/forester/java/src/org/forester/archaeopteryx/WebLink.java index 4db567e..3cab22b 100644 --- a/forester/java/src/org/forester/archaeopteryx/WebLink.java +++ b/forester/java/src/org/forester/archaeopteryx/WebLink.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java index ca0d111..066aebf 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableDomainArchitecture.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.phylogeny.data; diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java index b4f3868..9536554 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderablePhylogenyData.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.phylogeny.data; diff --git a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java index eb99a35..df16b75 100644 --- a/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java +++ b/forester/java/src/org/forester/archaeopteryx/phylogeny/data/RenderableVector.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.phylogeny.data; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java index 55a740d..25ed68a 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java index dc99878..839a328 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/Blast.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/Blast.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/GoAnnotation.java b/forester/java/src/org/forester/archaeopteryx/tools/GoAnnotation.java index 17d417f..702f30c 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/GoAnnotation.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/GoAnnotation.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java index b81cc25..7b51d56 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java index 32e21c8..d750a43 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhyloInferenceDialog.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java index b1ea597..f66cc25 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index f0ed725..10bc95e 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java index 60c531f..c9426d5 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/ProcessPool.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java b/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java index 2ca5f05..be2a9ec 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/ProcessRunning.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java index 454f139..6b9b88b 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/SequenceDataRetriver.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.tools; diff --git a/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java b/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java index 0d8b09c..232a215 100644 --- a/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java +++ b/forester/java/src/org/forester/archaeopteryx/webservices/PhylogeniesWebserviceClient.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.webservices; diff --git a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java index 86ff0d6..d619022 100644 --- a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java @@ -20,7 +20,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx.webservices; diff --git a/forester/java/src/org/forester/datastructures/Queue.java b/forester/java/src/org/forester/datastructures/Queue.java index c0c9c21..03e0f94 100644 --- a/forester/java/src/org/forester/datastructures/Queue.java +++ b/forester/java/src/org/forester/datastructures/Queue.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.datastructures; diff --git a/forester/java/src/org/forester/development/AbstractRenderer.java b/forester/java/src/org/forester/development/AbstractRenderer.java index 645735b..d3fe715 100644 --- a/forester/java/src/org/forester/development/AbstractRenderer.java +++ b/forester/java/src/org/forester/development/AbstractRenderer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/DevelopmentTools.java b/forester/java/src/org/forester/development/DevelopmentTools.java index 5a6a8db..3cbc385 100644 --- a/forester/java/src/org/forester/development/DevelopmentTools.java +++ b/forester/java/src/org/forester/development/DevelopmentTools.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/HmmerRest.java b/forester/java/src/org/forester/development/HmmerRest.java index b77aa23..f5ccf8e 100644 --- a/forester/java/src/org/forester/development/HmmerRest.java +++ b/forester/java/src/org/forester/development/HmmerRest.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/MsaRenderer.java b/forester/java/src/org/forester/development/MsaRenderer.java index 3f7b5a3..ee82c70 100644 --- a/forester/java/src/org/forester/development/MsaRenderer.java +++ b/forester/java/src/org/forester/development/MsaRenderer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/ResidueRenderer.java b/forester/java/src/org/forester/development/ResidueRenderer.java index 1e5122a..90f4dae 100644 --- a/forester/java/src/org/forester/development/ResidueRenderer.java +++ b/forester/java/src/org/forester/development/ResidueRenderer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/Test.java b/forester/java/src/org/forester/development/Test.java index a88d8f2..d929aa3 100644 --- a/forester/java/src/org/forester/development/Test.java +++ b/forester/java/src/org/forester/development/Test.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/development/Time.java b/forester/java/src/org/forester/development/Time.java index 9d9e8dc..11454f6 100644 --- a/forester/java/src/org/forester/development/Time.java +++ b/forester/java/src/org/forester/development/Time.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 9ff8457..3529d1e 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference; diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index 1f74a2b..c624bff 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.distance; diff --git a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java index f2b99a1..0dc6c6e 100644 --- a/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java +++ b/forester/java/src/org/forester/evoinference/distance/PairwiseDistanceCalculator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.distance; diff --git a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java index 2d5e7c7..4bf6a26 100644 --- a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.matrix.character; diff --git a/forester/java/src/org/forester/evoinference/matrix/character/CharacterStateMatrix.java b/forester/java/src/org/forester/evoinference/matrix/character/CharacterStateMatrix.java index 905552c..8d0af11 100644 --- a/forester/java/src/org/forester/evoinference/matrix/character/CharacterStateMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/character/CharacterStateMatrix.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.matrix.character; diff --git a/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java b/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java index a05e93d..7f80ceb 100644 --- a/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java +++ b/forester/java/src/org/forester/evoinference/matrix/character/DiscreteState.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.matrix.character; diff --git a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java index d45ecda..616a91c 100644 --- a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.matrix.distance; diff --git a/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java b/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java index 1a42fd3..2eeaca9 100644 --- a/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/distance/DistanceMatrix.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.matrix.distance; diff --git a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java index 65c072c..57df9c7 100644 --- a/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java +++ b/forester/java/src/org/forester/evoinference/parsimony/DolloParsimony.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.parsimony; diff --git a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java index 9d9a602..fd51681 100644 --- a/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java +++ b/forester/java/src/org/forester/evoinference/parsimony/FitchParsimony.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.parsimony; diff --git a/forester/java/src/org/forester/evoinference/tools/BootstrapResampler.java b/forester/java/src/org/forester/evoinference/tools/BootstrapResampler.java index 7837762..56fbc7c 100644 --- a/forester/java/src/org/forester/evoinference/tools/BootstrapResampler.java +++ b/forester/java/src/org/forester/evoinference/tools/BootstrapResampler.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference.tools; diff --git a/forester/java/src/org/forester/go/BasicGoRelationship.java b/forester/java/src/org/forester/go/BasicGoRelationship.java index 247e859..3a41d6d 100644 --- a/forester/java/src/org/forester/go/BasicGoRelationship.java +++ b/forester/java/src/org/forester/go/BasicGoRelationship.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/BasicGoSubset.java b/forester/java/src/org/forester/go/BasicGoSubset.java index 82015fb..f1658d7 100644 --- a/forester/java/src/org/forester/go/BasicGoSubset.java +++ b/forester/java/src/org/forester/go/BasicGoSubset.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/BasicGoTerm.java b/forester/java/src/org/forester/go/BasicGoTerm.java index 4401afe..f438d2f 100644 --- a/forester/java/src/org/forester/go/BasicGoTerm.java +++ b/forester/java/src/org/forester/go/BasicGoTerm.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/BasicGoXRef.java b/forester/java/src/org/forester/go/BasicGoXRef.java index b877bb4..c523102 100644 --- a/forester/java/src/org/forester/go/BasicGoXRef.java +++ b/forester/java/src/org/forester/go/BasicGoXRef.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoId.java b/forester/java/src/org/forester/go/GoId.java index cc02247..5f98e37 100644 --- a/forester/java/src/org/forester/go/GoId.java +++ b/forester/java/src/org/forester/go/GoId.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoNameSpace.java b/forester/java/src/org/forester/go/GoNameSpace.java index c9dc103..2d943c1 100644 --- a/forester/java/src/org/forester/go/GoNameSpace.java +++ b/forester/java/src/org/forester/go/GoNameSpace.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoRelationship.java b/forester/java/src/org/forester/go/GoRelationship.java index 47ef4e2..6ca8d7d 100644 --- a/forester/java/src/org/forester/go/GoRelationship.java +++ b/forester/java/src/org/forester/go/GoRelationship.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoSubset.java b/forester/java/src/org/forester/go/GoSubset.java index 1ee494c..02a2f03 100644 --- a/forester/java/src/org/forester/go/GoSubset.java +++ b/forester/java/src/org/forester/go/GoSubset.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoTerm.java b/forester/java/src/org/forester/go/GoTerm.java index 600cb41..71a75cf 100644 --- a/forester/java/src/org/forester/go/GoTerm.java +++ b/forester/java/src/org/forester/go/GoTerm.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoUtils.java b/forester/java/src/org/forester/go/GoUtils.java index 39a778f..adec9fb 100644 --- a/forester/java/src/org/forester/go/GoUtils.java +++ b/forester/java/src/org/forester/go/GoUtils.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/GoXRef.java b/forester/java/src/org/forester/go/GoXRef.java index 7f0a5e5..e0a4ca8 100644 --- a/forester/java/src/org/forester/go/GoXRef.java +++ b/forester/java/src/org/forester/go/GoXRef.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/Mapping.java b/forester/java/src/org/forester/go/Mapping.java index 440094f..5e9377a 100644 --- a/forester/java/src/org/forester/go/Mapping.java +++ b/forester/java/src/org/forester/go/Mapping.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/OBOparser.java b/forester/java/src/org/forester/go/OBOparser.java index b47a60b..d2486db 100644 --- a/forester/java/src/org/forester/go/OBOparser.java +++ b/forester/java/src/org/forester/go/OBOparser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/PfamToGoMapping.java b/forester/java/src/org/forester/go/PfamToGoMapping.java index 27ea75d..e11fde1 100644 --- a/forester/java/src/org/forester/go/PfamToGoMapping.java +++ b/forester/java/src/org/forester/go/PfamToGoMapping.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/TestGo.java b/forester/java/src/org/forester/go/TestGo.java index 8607c35..f8197ee 100644 --- a/forester/java/src/org/forester/go/TestGo.java +++ b/forester/java/src/org/forester/go/TestGo.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go; diff --git a/forester/java/src/org/forester/go/etc/MetaOntologizer.java b/forester/java/src/org/forester/go/etc/MetaOntologizer.java index c77f9e5..11afb54 100644 --- a/forester/java/src/org/forester/go/etc/MetaOntologizer.java +++ b/forester/java/src/org/forester/go/etc/MetaOntologizer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.go.etc; diff --git a/forester/java/src/org/forester/io/parsers/FastaParser.java b/forester/java/src/org/forester/io/parsers/FastaParser.java index 6a652f5..348bec4 100644 --- a/forester/java/src/org/forester/io/parsers/FastaParser.java +++ b/forester/java/src/org/forester/io/parsers/FastaParser.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java index bf6577c..507ae1f 100644 --- a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java +++ b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java index 4c9914e..090a052 100644 --- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java index b5d1bc1..ada802a 100644 --- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/PhylogenyParser.java b/forester/java/src/org/forester/io/parsers/PhylogenyParser.java index d4bbdb4..b0fe08a 100644 --- a/forester/java/src/org/forester/io/parsers/PhylogenyParser.java +++ b/forester/java/src/org/forester/io/parsers/PhylogenyParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java index 03f66df..78b9fcd 100644 --- a/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java +++ b/forester/java/src/org/forester/io/parsers/SymmetricalDistanceMatrixParser.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers; diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java b/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java index a9d9d3d..721bcc6 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusBinaryStatesMatrixParser.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester/ +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester/ package org.forester.io.parsers.nexus; diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusConstants.java b/forester/java/src/org/forester/io/parsers/nexus/NexusConstants.java index 4c4f67b..250cfb4 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusConstants.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusConstants.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nexus; diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusFormatException.java b/forester/java/src/org/forester/io/parsers/nexus/NexusFormatException.java index cbc15db..dcf9c37 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusFormatException.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusFormatException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nexus; diff --git a/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java b/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java index 8b6e638..0f9a5b6 100644 --- a/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java +++ b/forester/java/src/org/forester/io/parsers/nexus/NexusPhylogeniesParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nexus; diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXFormatException.java b/forester/java/src/org/forester/io/parsers/nhx/NHXFormatException.java index 24a11b1..2091965 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXFormatException.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXFormatException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nhx; diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java index 5971bfc..1463d84 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nhx; diff --git a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java index 3a524bb..00cba9d 100644 --- a/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java +++ b/forester/java/src/org/forester/io/parsers/nhx/NHXtags.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.nhx; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java index 5dcd5a8..7bb41d9 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlDataFormatException.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlException.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlException.java index 3181688..722ea37 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlException.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java index b724a79..ec05952 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlHandler.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java index 4659fc2..9e72a30 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlMapping.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java index b8de6cf..983048f 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java index dadaea5..f7aa962 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/PhyloXmlUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java b/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java index 27df49c..e0cc08c 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/XmlElement.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java index 88a6e8b..cab3bef 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/AnnotationParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java index 1d22594..d8692f0 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/BinaryCharactersParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java index 05f08d7..6a709f6 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/BranchWidthParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java index fa4a661..65e6658 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java index 72bc11d..917efe9 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ConfidenceParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/DateParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/DateParser.java index 780b84d..0c4040a 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/DateParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/DateParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/DistributionParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/DistributionParser.java index 904204d..a01f205 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/DistributionParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/DistributionParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java index e76ba6a..4010912 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/DomainArchitectureParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/EventParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/EventParser.java index 5c2ee69..99b2bd3 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/EventParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/EventParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java index f74220e..e12b92a 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/PhylogenyDataPhyloXmlParser.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/PointParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/PointParser.java index e795460..c7006ab 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/PointParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/PointParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/PolygonParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/PolygonParser.java index 447a641..b996f09 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/PolygonParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/PolygonParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java index 75498cd..e6a15df 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ProteinDomainParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java index 5208b9f..fa1caad 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java index 624944d..468adc9 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/SequenceRelationParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java index a9ffca2..f55028f 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/TaxonomyParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/UriParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/UriParser.java index 40f5fa3..bc032f8 100644 --- a/forester/java/src/org/forester/io/parsers/phyloxml/data/UriParser.java +++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/UriParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.phyloxml.data; diff --git a/forester/java/src/org/forester/io/parsers/tol/TolParser.java b/forester/java/src/org/forester/io/parsers/tol/TolParser.java index 24aeeba..de48b4c 100644 --- a/forester/java/src/org/forester/io/parsers/tol/TolParser.java +++ b/forester/java/src/org/forester/io/parsers/tol/TolParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.tol; diff --git a/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java b/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java index 975ca0d..3575986 100644 --- a/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java +++ b/forester/java/src/org/forester/io/parsers/tol/TolXmlHandler.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.tol; diff --git a/forester/java/src/org/forester/io/parsers/tol/TolXmlMapping.java b/forester/java/src/org/forester/io/parsers/tol/TolXmlMapping.java index bb7732d..165d9c0 100644 --- a/forester/java/src/org/forester/io/parsers/tol/TolXmlMapping.java +++ b/forester/java/src/org/forester/io/parsers/tol/TolXmlMapping.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.tol; diff --git a/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java b/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java index c94a60f..d4dc9b7 100644 --- a/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java +++ b/forester/java/src/org/forester/io/parsers/util/PhylogenyParserException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.parsers.util; diff --git a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java index 67d38d4..f072c58 100644 --- a/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java +++ b/forester/java/src/org/forester/io/writers/PhyloXmlNodeWriter.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.writers; diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java index 7e03ef3..454ca74 100644 --- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java +++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.io.writers; diff --git a/forester/java/src/org/forester/msa/BasicMsa.java b/forester/java/src/org/forester/msa/BasicMsa.java index 907d212..5fc2590 100644 --- a/forester/java/src/org/forester/msa/BasicMsa.java +++ b/forester/java/src/org/forester/msa/BasicMsa.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/ClustalOmega.java b/forester/java/src/org/forester/msa/ClustalOmega.java index 938fc78..417e889 100644 --- a/forester/java/src/org/forester/msa/ClustalOmega.java +++ b/forester/java/src/org/forester/msa/ClustalOmega.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/Mafft.java b/forester/java/src/org/forester/msa/Mafft.java index ec72c0d..ae9fdf1 100644 --- a/forester/java/src/org/forester/msa/Mafft.java +++ b/forester/java/src/org/forester/msa/Mafft.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/Msa.java b/forester/java/src/org/forester/msa/Msa.java index 790b674..1eb9533 100644 --- a/forester/java/src/org/forester/msa/Msa.java +++ b/forester/java/src/org/forester/msa/Msa.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/MsaFormatException.java b/forester/java/src/org/forester/msa/MsaFormatException.java index 791ccd9..1ae1bfc 100644 --- a/forester/java/src/org/forester/msa/MsaFormatException.java +++ b/forester/java/src/org/forester/msa/MsaFormatException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/MsaInferrer.java b/forester/java/src/org/forester/msa/MsaInferrer.java index 8c839f9..55aa7f7 100644 --- a/forester/java/src/org/forester/msa/MsaInferrer.java +++ b/forester/java/src/org/forester/msa/MsaInferrer.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/MsaMethods.java b/forester/java/src/org/forester/msa/MsaMethods.java index ee9338b..06ca50b 100644 --- a/forester/java/src/org/forester/msa/MsaMethods.java +++ b/forester/java/src/org/forester/msa/MsaMethods.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/msa/ResampleableMsa.java b/forester/java/src/org/forester/msa/ResampleableMsa.java index ad36c53..b7c8a7d 100644 --- a/forester/java/src/org/forester/msa/ResampleableMsa.java +++ b/forester/java/src/org/forester/msa/ResampleableMsa.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa; diff --git a/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java b/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java index 9df3549..83fcda5 100644 --- a/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java +++ b/forester/java/src/org/forester/pccx/BasicExternalNodeBasedCoverageExtender.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java index f1b2268..00b4d48 100644 --- a/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/BranchCountingBasedScoringMethod.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java b/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java index 2b14bf4..5086f7d 100644 --- a/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/BranchLengthBasedScoringMethod.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/Coverage.java b/forester/java/src/org/forester/pccx/Coverage.java index c5d90ff..685333a 100644 --- a/forester/java/src/org/forester/pccx/Coverage.java +++ b/forester/java/src/org/forester/pccx/Coverage.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/CoverageCalculationMethod.java b/forester/java/src/org/forester/pccx/CoverageCalculationMethod.java index 265e284..4ef0b78 100644 --- a/forester/java/src/org/forester/pccx/CoverageCalculationMethod.java +++ b/forester/java/src/org/forester/pccx/CoverageCalculationMethod.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/CoverageCalculationOptions.java b/forester/java/src/org/forester/pccx/CoverageCalculationOptions.java index c757c3b..1249d11 100644 --- a/forester/java/src/org/forester/pccx/CoverageCalculationOptions.java +++ b/forester/java/src/org/forester/pccx/CoverageCalculationOptions.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/CoverageCalculator.java b/forester/java/src/org/forester/pccx/CoverageCalculator.java index 2f16ae1..2031778 100644 --- a/forester/java/src/org/forester/pccx/CoverageCalculator.java +++ b/forester/java/src/org/forester/pccx/CoverageCalculator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/CoverageExtender.java b/forester/java/src/org/forester/pccx/CoverageExtender.java index 335b99b..dec2298 100644 --- a/forester/java/src/org/forester/pccx/CoverageExtender.java +++ b/forester/java/src/org/forester/pccx/CoverageExtender.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverage.java b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverage.java index d56917b..661fd0a 100644 --- a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverage.java +++ b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverage.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java index a88018f..5e73593 100644 --- a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java +++ b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethod.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java index 70b7265..bd5da8b 100644 --- a/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java +++ b/forester/java/src/org/forester/pccx/ExternalNodeBasedCoverageMethodOptions.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java b/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java index 62b4390..7ba40cb 100644 --- a/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java +++ b/forester/java/src/org/forester/pccx/LogBranchLengthBasedScoringMethod.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/ModelingUtils.java b/forester/java/src/org/forester/pccx/ModelingUtils.java index 929f2e1..f8d4062 100644 --- a/forester/java/src/org/forester/pccx/ModelingUtils.java +++ b/forester/java/src/org/forester/pccx/ModelingUtils.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java index 5fab38a..d34fa09 100644 --- a/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java +++ b/forester/java/src/org/forester/pccx/ScoringMethodForExternalNode.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/pccx/TestPccx.java b/forester/java/src/org/forester/pccx/TestPccx.java index 642d919..2e36f25 100644 --- a/forester/java/src/org/forester/pccx/TestPccx.java +++ b/forester/java/src/org/forester/pccx/TestPccx.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.pccx; diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index aaa0fd3..67cdeb5 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny; diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyBranch.java b/forester/java/src/org/forester/phylogeny/PhylogenyBranch.java index 5752fbf..4b9c673 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyBranch.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyBranch.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny; diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java index f2a982d..d87188b 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny; diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java index 819ba7a..9663845 100644 --- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java +++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny; diff --git a/forester/java/src/org/forester/phylogeny/data/Annotation.java b/forester/java/src/org/forester/phylogeny/data/Annotation.java index 829707a..260c055 100644 --- a/forester/java/src/org/forester/phylogeny/data/Annotation.java +++ b/forester/java/src/org/forester/phylogeny/data/Annotation.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java index add1dfa..cea856f 100644 --- a/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java +++ b/forester/java/src/org/forester/phylogeny/data/BinaryCharacters.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/BranchColor.java b/forester/java/src/org/forester/phylogeny/data/BranchColor.java index 84a356b..50d7054 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchColor.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchColor.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/BranchData.java b/forester/java/src/org/forester/phylogeny/data/BranchData.java index 6a517b8..68f8e2c 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchData.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchData.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/BranchWidth.java b/forester/java/src/org/forester/phylogeny/data/BranchWidth.java index cfdf90d..cc7d853 100644 --- a/forester/java/src/org/forester/phylogeny/data/BranchWidth.java +++ b/forester/java/src/org/forester/phylogeny/data/BranchWidth.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Confidence.java b/forester/java/src/org/forester/phylogeny/data/Confidence.java index e9e631a..4ea14ef 100644 --- a/forester/java/src/org/forester/phylogeny/data/Confidence.java +++ b/forester/java/src/org/forester/phylogeny/data/Confidence.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Date.java b/forester/java/src/org/forester/phylogeny/data/Date.java index af70f80..5cd1039 100644 --- a/forester/java/src/org/forester/phylogeny/data/Date.java +++ b/forester/java/src/org/forester/phylogeny/data/Date.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Distribution.java b/forester/java/src/org/forester/phylogeny/data/Distribution.java index e799d82..0616f94 100644 --- a/forester/java/src/org/forester/phylogeny/data/Distribution.java +++ b/forester/java/src/org/forester/phylogeny/data/Distribution.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java index 3dcf02a..0f09c55 100644 --- a/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java +++ b/forester/java/src/org/forester/phylogeny/data/DomainArchitecture.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Event.java b/forester/java/src/org/forester/phylogeny/data/Event.java index c362f7c..afd714c 100644 --- a/forester/java/src/org/forester/phylogeny/data/Event.java +++ b/forester/java/src/org/forester/phylogeny/data/Event.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Identifier.java b/forester/java/src/org/forester/phylogeny/data/Identifier.java index 97297f8..8a897af 100644 --- a/forester/java/src/org/forester/phylogeny/data/Identifier.java +++ b/forester/java/src/org/forester/phylogeny/data/Identifier.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/MultipleUris.java b/forester/java/src/org/forester/phylogeny/data/MultipleUris.java index acf9ca0..fcde7d4 100644 --- a/forester/java/src/org/forester/phylogeny/data/MultipleUris.java +++ b/forester/java/src/org/forester/phylogeny/data/MultipleUris.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java index bc7e8b9..6677f0f 100644 --- a/forester/java/src/org/forester/phylogeny/data/NodeData.java +++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java index 0bf8484..2db9364 100644 --- a/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java +++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyData.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java index f129259..09707cd 100644 --- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java +++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Polygon.java b/forester/java/src/org/forester/phylogeny/data/Polygon.java index 577a532..feed628 100644 --- a/forester/java/src/org/forester/phylogeny/data/Polygon.java +++ b/forester/java/src/org/forester/phylogeny/data/Polygon.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/PropertiesMap.java b/forester/java/src/org/forester/phylogeny/data/PropertiesMap.java index 1a9d6a1..0f47f27 100644 --- a/forester/java/src/org/forester/phylogeny/data/PropertiesMap.java +++ b/forester/java/src/org/forester/phylogeny/data/PropertiesMap.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Property.java b/forester/java/src/org/forester/phylogeny/data/Property.java index ff14b0f..b7b7c17 100644 --- a/forester/java/src/org/forester/phylogeny/data/Property.java +++ b/forester/java/src/org/forester/phylogeny/data/Property.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java b/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java index 5964f47..3adcdfd 100644 --- a/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java +++ b/forester/java/src/org/forester/phylogeny/data/ProteinDomain.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Sequence.java b/forester/java/src/org/forester/phylogeny/data/Sequence.java index b549890..b9e6aa3 100644 --- a/forester/java/src/org/forester/phylogeny/data/Sequence.java +++ b/forester/java/src/org/forester/phylogeny/data/Sequence.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java b/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java index b8ba724..45134e4 100644 --- a/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java +++ b/forester/java/src/org/forester/phylogeny/data/SequenceRelation.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java index 544522b..b354921 100644 --- a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java +++ b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/data/Uri.java b/forester/java/src/org/forester/phylogeny/data/Uri.java index 118a8e4..fb97b22 100644 --- a/forester/java/src/org/forester/phylogeny/data/Uri.java +++ b/forester/java/src/org/forester/phylogeny/data/Uri.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.data; diff --git a/forester/java/src/org/forester/phylogeny/factories/BasicPhylogenyFactory.java b/forester/java/src/org/forester/phylogeny/factories/BasicPhylogenyFactory.java index dbe565e..d0abe40 100644 --- a/forester/java/src/org/forester/phylogeny/factories/BasicPhylogenyFactory.java +++ b/forester/java/src/org/forester/phylogeny/factories/BasicPhylogenyFactory.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.factories; diff --git a/forester/java/src/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java b/forester/java/src/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java index 1828852..14f2f20 100644 --- a/forester/java/src/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java +++ b/forester/java/src/org/forester/phylogeny/factories/ParserBasedPhylogenyFactory.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.factories; diff --git a/forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java b/forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java index 565e31a..7b2eac9 100644 --- a/forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java +++ b/forester/java/src/org/forester/phylogeny/factories/PhylogenyFactory.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.factories; diff --git a/forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java b/forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java index 4e6df65..35a02aa 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java +++ b/forester/java/src/org/forester/phylogeny/iterators/ExternalForwardIterator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java b/forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java index f5ab499..cc8e11b 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java +++ b/forester/java/src/org/forester/phylogeny/iterators/LevelOrderTreeIterator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java b/forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java index f10aecd..1fa01bd 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java +++ b/forester/java/src/org/forester/phylogeny/iterators/PhylogenyNodeIterator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java b/forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java index ae291ee..a3f004f 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java +++ b/forester/java/src/org/forester/phylogeny/iterators/PostOrderStackObject.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/phylogeny/iterators/PostorderTreeIterator.java b/forester/java/src/org/forester/phylogeny/iterators/PostorderTreeIterator.java index 737a75d..9819b58 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/PostorderTreeIterator.java +++ b/forester/java/src/org/forester/phylogeny/iterators/PostorderTreeIterator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java b/forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java index c4e06f0..9d6f690 100644 --- a/forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java +++ b/forester/java/src/org/forester/phylogeny/iterators/PreorderTreeIterator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.phylogeny.iterators; diff --git a/forester/java/src/org/forester/protein/BasicDomain.java b/forester/java/src/org/forester/protein/BasicDomain.java index c6c5288..0232b91 100644 --- a/forester/java/src/org/forester/protein/BasicDomain.java +++ b/forester/java/src/org/forester/protein/BasicDomain.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/BasicProtein.java b/forester/java/src/org/forester/protein/BasicProtein.java index b364e29..9b688c9 100644 --- a/forester/java/src/org/forester/protein/BasicProtein.java +++ b/forester/java/src/org/forester/protein/BasicProtein.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/BinaryDomainCombination.java b/forester/java/src/org/forester/protein/BinaryDomainCombination.java index 02bd7f8..1098644 100644 --- a/forester/java/src/org/forester/protein/BinaryDomainCombination.java +++ b/forester/java/src/org/forester/protein/BinaryDomainCombination.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/Domain.java b/forester/java/src/org/forester/protein/Domain.java index c2a09b9..3ede985 100644 --- a/forester/java/src/org/forester/protein/Domain.java +++ b/forester/java/src/org/forester/protein/Domain.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/DomainId.java b/forester/java/src/org/forester/protein/DomainId.java index 72bb39b..89a23cf 100644 --- a/forester/java/src/org/forester/protein/DomainId.java +++ b/forester/java/src/org/forester/protein/DomainId.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java index a4512df..7206545 100644 --- a/forester/java/src/org/forester/protein/Protein.java +++ b/forester/java/src/org/forester/protein/Protein.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/protein/ProteinId.java b/forester/java/src/org/forester/protein/ProteinId.java index 0319e99..bb13c6b 100644 --- a/forester/java/src/org/forester/protein/ProteinId.java +++ b/forester/java/src/org/forester/protein/ProteinId.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.protein; diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java index d844d2b..cf5475f 100644 --- a/forester/java/src/org/forester/rio/RIO.java +++ b/forester/java/src/org/forester/rio/RIO.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.rio; diff --git a/forester/java/src/org/forester/sdi/GSDI.java b/forester/java/src/org/forester/sdi/GSDI.java index 63c6215..9f95b24 100644 --- a/forester/java/src/org/forester/sdi/GSDI.java +++ b/forester/java/src/org/forester/sdi/GSDI.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; diff --git a/forester/java/src/org/forester/sdi/SDI.java b/forester/java/src/org/forester/sdi/SDI.java index 0bb74d3..2c59efa 100644 --- a/forester/java/src/org/forester/sdi/SDI.java +++ b/forester/java/src/org/forester/sdi/SDI.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java index 7af2359..85481ff 100644 --- a/forester/java/src/org/forester/sdi/SDIR.java +++ b/forester/java/src/org/forester/sdi/SDIR.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; diff --git a/forester/java/src/org/forester/sdi/TestGSDI.java b/forester/java/src/org/forester/sdi/TestGSDI.java index e7a9b46..4e39e5c 100644 --- a/forester/java/src/org/forester/sdi/TestGSDI.java +++ b/forester/java/src/org/forester/sdi/TestGSDI.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sdi; diff --git a/forester/java/src/org/forester/sequence/BasicSequence.java b/forester/java/src/org/forester/sequence/BasicSequence.java index 6b76f92..4a4662a 100644 --- a/forester/java/src/org/forester/sequence/BasicSequence.java +++ b/forester/java/src/org/forester/sequence/BasicSequence.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sequence; diff --git a/forester/java/src/org/forester/sequence/Sequence.java b/forester/java/src/org/forester/sequence/Sequence.java index 90f3b04..3e2473a 100644 --- a/forester/java/src/org/forester/sequence/Sequence.java +++ b/forester/java/src/org/forester/sequence/Sequence.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.sequence; diff --git a/forester/java/src/org/forester/species/BasicSpecies.java b/forester/java/src/org/forester/species/BasicSpecies.java index 136b507..326c661 100644 --- a/forester/java/src/org/forester/species/BasicSpecies.java +++ b/forester/java/src/org/forester/species/BasicSpecies.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.species; diff --git a/forester/java/src/org/forester/species/Species.java b/forester/java/src/org/forester/species/Species.java index b54e5eb..b5331df 100644 --- a/forester/java/src/org/forester/species/Species.java +++ b/forester/java/src/org/forester/species/Species.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.species; diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java index 3da8ed4..9d9a441 100644 --- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java index 67e5ffd..39c7450 100644 --- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java index 23f3058..300a4ed 100644 --- a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java index 69adcb9..9a9bbfb 100644 --- a/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/BasicDomainSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java index d90eed4..28ca259 100644 --- a/forester/java/src/org/forester/surfacing/CombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java index 3b0c6dc..f271afa 100644 --- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java index 965f595..27327b6 100644 --- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java index a037ed5..81fdce7 100644 --- a/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/CountsBasedPairwiseDomainSimilarity.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java index e57e137..2e5d797 100644 --- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java index 1f2a674..16c2940 100644 --- a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java index 1461963..cdc9416 100644 --- a/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainArchitectureBasedGenomeSimilarityCalculator.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java index c61dcad..6077ffc 100644 --- a/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java index 1a742fd..20a25d4 100644 --- a/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java +++ b/forester/java/src/org/forester/surfacing/DomainCountsDifferenceUtil.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainLengths.java b/forester/java/src/org/forester/surfacing/DomainLengths.java index 37ebfdc..7e628ce 100644 --- a/forester/java/src/org/forester/surfacing/DomainLengths.java +++ b/forester/java/src/org/forester/surfacing/DomainLengths.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java index cbd14b0..9a9e0a7 100644 --- a/forester/java/src/org/forester/surfacing/DomainLengthsTable.java +++ b/forester/java/src/org/forester/surfacing/DomainLengthsTable.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java index 4b7303d..e2e0af3 100644 --- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarity.java b/forester/java/src/org/forester/surfacing/DomainSimilarity.java index fc21dda..b9e9860 100644 --- a/forester/java/src/org/forester/surfacing/DomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/DomainSimilarity.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java index 27ea841..fa0ea62 100644 --- a/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/DomainSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java index 245f565..f444ff7 100644 --- a/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java +++ b/forester/java/src/org/forester/surfacing/GenomeWideCombinableDomains.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java index 8880b05..2fa6f4e 100644 --- a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarity.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java index 291a350..58fd1a1 100644 --- a/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/PairwiseDomainSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java index 4c3e442..6281764 100644 --- a/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java +++ b/forester/java/src/org/forester/surfacing/PairwiseGenomeComparator.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java index d4d23db..6966aee 100644 --- a/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java +++ b/forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java index 7317338..28ca512 100644 --- a/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java +++ b/forester/java/src/org/forester/surfacing/PrintableSpeciesSpecificDomainSimilariyData.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java index fbcedb6..309d321 100644 --- a/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java +++ b/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/SimpleDomain.java b/forester/java/src/org/forester/surfacing/SimpleDomain.java index 74173df..5182865 100644 --- a/forester/java/src/org/forester/surfacing/SimpleDomain.java +++ b/forester/java/src/org/forester/surfacing/SimpleDomain.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java b/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java index 1e72929..d605344 100644 --- a/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java +++ b/forester/java/src/org/forester/surfacing/SpeciesSpecificDomainSimilariyData.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/SurfacingConstants.java b/forester/java/src/org/forester/surfacing/SurfacingConstants.java index c78f157..c1991f6 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingConstants.java +++ b/forester/java/src/org/forester/surfacing/SurfacingConstants.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java index 6c036fd..06c8ca0 100644 --- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java +++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java index 5cdd6eb..f243dab 100644 --- a/forester/java/src/org/forester/surfacing/TestSurfacing.java +++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.surfacing; diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java index 7960f72..e4bec20 100644 --- a/forester/java/src/org/forester/test/Test.java +++ b/forester/java/src/org/forester/test/Test.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test; diff --git a/forester/java/src/org/forester/test/examples/Example1.java b/forester/java/src/org/forester/test/examples/Example1.java index cd65138..63536b7 100644 --- a/forester/java/src/org/forester/test/examples/Example1.java +++ b/forester/java/src/org/forester/test/examples/Example1.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test.examples; diff --git a/forester/java/src/org/forester/test/examples/Example2.java b/forester/java/src/org/forester/test/examples/Example2.java index 221ed0b..6f9cfa1 100644 --- a/forester/java/src/org/forester/test/examples/Example2.java +++ b/forester/java/src/org/forester/test/examples/Example2.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test.examples; diff --git a/forester/java/src/org/forester/test/examples/Example3.java b/forester/java/src/org/forester/test/examples/Example3.java index d5c2bb6..60354f4 100644 --- a/forester/java/src/org/forester/test/examples/Example3.java +++ b/forester/java/src/org/forester/test/examples/Example3.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test.examples; diff --git a/forester/java/src/org/forester/test/examples/Example4.java b/forester/java/src/org/forester/test/examples/Example4.java index 2c5cb17..7f35850 100644 --- a/forester/java/src/org/forester/test/examples/Example4.java +++ b/forester/java/src/org/forester/test/examples/Example4.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test.examples; diff --git a/forester/java/src/org/forester/test/examples/Example5.java b/forester/java/src/org/forester/test/examples/Example5.java index facc4b9..09935c8 100644 --- a/forester/java/src/org/forester/test/examples/Example5.java +++ b/forester/java/src/org/forester/test/examples/Example5.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.test.examples; diff --git a/forester/java/src/org/forester/tools/ConfidenceAssessor.java b/forester/java/src/org/forester/tools/ConfidenceAssessor.java index 1a9d85e..2dc710c 100644 --- a/forester/java/src/org/forester/tools/ConfidenceAssessor.java +++ b/forester/java/src/org/forester/tools/ConfidenceAssessor.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.tools; diff --git a/forester/java/src/org/forester/tools/PhylogenyDecorator.java b/forester/java/src/org/forester/tools/PhylogenyDecorator.java index f9bcd1f..f4f6c1a 100644 --- a/forester/java/src/org/forester/tools/PhylogenyDecorator.java +++ b/forester/java/src/org/forester/tools/PhylogenyDecorator.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.tools; diff --git a/forester/java/src/org/forester/tools/SupportCount.java b/forester/java/src/org/forester/tools/SupportCount.java index 5c8e924..50702d4 100644 --- a/forester/java/src/org/forester/tools/SupportCount.java +++ b/forester/java/src/org/forester/tools/SupportCount.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.tools; diff --git a/forester/java/src/org/forester/tools/TreeSplitMatrix.java b/forester/java/src/org/forester/tools/TreeSplitMatrix.java index ebd8792..58d6eb6 100644 --- a/forester/java/src/org/forester/tools/TreeSplitMatrix.java +++ b/forester/java/src/org/forester/tools/TreeSplitMatrix.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.tools; diff --git a/forester/java/src/org/forester/util/AsciiHistogram.java b/forester/java/src/org/forester/util/AsciiHistogram.java index f9b0bb3..7c8082f 100644 --- a/forester/java/src/org/forester/util/AsciiHistogram.java +++ b/forester/java/src/org/forester/util/AsciiHistogram.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java index 240d439..057b388 100644 --- a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java +++ b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/BasicTableParser.java b/forester/java/src/org/forester/util/BasicTableParser.java index 2917a31..aaa5781 100644 --- a/forester/java/src/org/forester/util/BasicTableParser.java +++ b/forester/java/src/org/forester/util/BasicTableParser.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/CommandLineArguments.java b/forester/java/src/org/forester/util/CommandLineArguments.java index 91f11bd..7e2a167 100644 --- a/forester/java/src/org/forester/util/CommandLineArguments.java +++ b/forester/java/src/org/forester/util/CommandLineArguments.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/CommandProcessBuilder.java b/forester/java/src/org/forester/util/CommandProcessBuilder.java index 645a6cd..b5887a8 100644 --- a/forester/java/src/org/forester/util/CommandProcessBuilder.java +++ b/forester/java/src/org/forester/util/CommandProcessBuilder.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/DescriptiveStatistics.java b/forester/java/src/org/forester/util/DescriptiveStatistics.java index 014b530..beeade9 100644 --- a/forester/java/src/org/forester/util/DescriptiveStatistics.java +++ b/forester/java/src/org/forester/util/DescriptiveStatistics.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/ExternalProgram.java b/forester/java/src/org/forester/util/ExternalProgram.java index 7a76b6b..d28e31d 100644 --- a/forester/java/src/org/forester/util/ExternalProgram.java +++ b/forester/java/src/org/forester/util/ExternalProgram.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/FailedConditionCheckException.java b/forester/java/src/org/forester/util/FailedConditionCheckException.java index cad5191..82c65c1 100644 --- a/forester/java/src/org/forester/util/FailedConditionCheckException.java +++ b/forester/java/src/org/forester/util/FailedConditionCheckException.java @@ -22,7 +22,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/ForesterConstants.java b/forester/java/src/org/forester/util/ForesterConstants.java index 34b2322..897fb7a 100644 --- a/forester/java/src/org/forester/util/ForesterConstants.java +++ b/forester/java/src/org/forester/util/ForesterConstants.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java index cb04e65..caf4045 100644 --- a/forester/java/src/org/forester/util/ForesterUtil.java +++ b/forester/java/src/org/forester/util/ForesterUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/IllegalFormatUseException.java b/forester/java/src/org/forester/util/IllegalFormatUseException.java index 437d548..6580cf9 100644 --- a/forester/java/src/org/forester/util/IllegalFormatUseException.java +++ b/forester/java/src/org/forester/util/IllegalFormatUseException.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/SequenceIdParser.java b/forester/java/src/org/forester/util/SequenceIdParser.java index 3b6bc5d..c96d0f4 100644 --- a/forester/java/src/org/forester/util/SequenceIdParser.java +++ b/forester/java/src/org/forester/util/SequenceIdParser.java @@ -24,7 +24,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/util/WindowsUtils.java b/forester/java/src/org/forester/util/WindowsUtils.java index 9fa599f..b65d9fe 100644 --- a/forester/java/src/org/forester/util/WindowsUtils.java +++ b/forester/java/src/org/forester/util/WindowsUtils.java @@ -19,7 +19,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.util; diff --git a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java index d845951..c8131ad 100644 --- a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java +++ b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.seqdb; diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDatabaseEntry.java b/forester/java/src/org/forester/ws/seqdb/SequenceDatabaseEntry.java index 9ae7892..46c5fdf 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDatabaseEntry.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDatabaseEntry.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.seqdb; diff --git a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java index 5004a47..c2258d6 100644 --- a/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java +++ b/forester/java/src/org/forester/ws/seqdb/SequenceDbWsTools.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.seqdb; diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java index fc85037..263a115 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtEntry.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.seqdb; diff --git a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java index 0884a6f..b50d41e 100644 --- a/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java +++ b/forester/java/src/org/forester/ws/seqdb/UniProtTaxonomy.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.seqdb; diff --git a/forester/java/src/org/forester/ws/wabi/RestUtil.java b/forester/java/src/org/forester/ws/wabi/RestUtil.java index fe4a8ee..cce2569 100644 --- a/forester/java/src/org/forester/ws/wabi/RestUtil.java +++ b/forester/java/src/org/forester/ws/wabi/RestUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.wabi; diff --git a/forester/java/src/org/forester/ws/wabi/TxSearch.java b/forester/java/src/org/forester/ws/wabi/TxSearch.java index e4a5b25..78ac76c 100644 --- a/forester/java/src/org/forester/ws/wabi/TxSearch.java +++ b/forester/java/src/org/forester/ws/wabi/TxSearch.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.wabi; diff --git a/forester/java/src/org/forester/ws/wabi/WabiTools.java b/forester/java/src/org/forester/ws/wabi/WabiTools.java index c1a2e79..b5a94dc 100644 --- a/forester/java/src/org/forester/ws/wabi/WabiTools.java +++ b/forester/java/src/org/forester/ws/wabi/WabiTools.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.ws.wabi;