Use consistent line endings in source code

Author: arteymix

gemma-cli/src/main/java/ubic/gemma/apps/BioSequenceCleanupCli.java

@@ -1,181 +1,181 @@
-/*
- * The Gemma project
- *
- * Copyright (c) 2011 University of British Columbia
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *       http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- */
-
-package ubic.gemma.core.analysis.preprocess.batcheffects;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.text.DateFormat;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.Locale;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-/**
- * @author paul
- */
-@SuppressWarnings("WeakerAccess") // Possibly accessed via CLI tools
-public abstract class BaseScanDateExtractor implements ScanDateExtractor {
-
-    protected static final String GENEPIX_DATETIME_HEADER_REGEXP = "\"?DateTime=.*";
-    private static final String STANDARD_FORMAT_REGEX_2 = ".+?([0-9]{2}[/-][0-9]{2}[/-]\\s[0-9]\\s[0-9]{2}:[0-9]{2}:[0-9]{2}).+";
-    private static final String STANDARD_FORMAT_REGEX = ".+?([0-9]{2}[/-][0-9]{2}[/-][0-9]{2}\\s[0-9]{2}:[0-9]{2}:[0-9]{2}).+";
-    private static final String LONG_FORMAT_REGEX = "\\s*Date\\s*(.+)";
-    private static final Log log = LogFactory.getLog( BaseScanDateExtractor.class );
-
-    /**
-     * This method should be generic for GenePix/GPR/ATR file formats. Has DateType at the top formatted with quotes:
-     * "DateTime=2005/11/09 11:36:27". Example GSE15739
-     * For more information see <a href='http://mdc.custhelp.com/app/answers/detail/a_id/18886'>here</a>.
-     *
-     * @param reader the reader
-     * @return date
-     * @throws IOException when there was a read error
-     */
-    protected Date extractGenePix( BufferedReader reader ) throws IOException {
-        String line;
-        // GPR/ATF file. Read a few lines to find the datetime (the header tells us how long the header is, but
-        // this is probably okay)
-        Date d = null;
-        while ( ( line = reader.readLine() ) != null ) {
-
-            if ( line.matches( BaseScanDateExtractor.GENEPIX_DATETIME_HEADER_REGEXP ) ) {
-                d = this.parseGenePixDateTime( line );
-                break;
-            }
-        }
-
-        if ( d == null ) {
-            throw new IllegalStateException( "Failed to find the 'DateTime' line" );
-        }
-        reader.close();
-        return d;
-    }
-
-    /**
-     * @param line like "DateTime=2005/11/09 11:36:27" (with the quotes) possibly with trailing whitespace.
-     * @return date
-     */
-    protected Date parseGenePixDateTime( String line ) {
-        String dateString = line.trim().replaceAll( "\"", "" ).replaceFirst( "DateTime=", "" );
-        try {
-
-            DateFormat f = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss", Locale.ENGLISH ); // 2005/11/09 11:36:27, 2006/04/07 14:18:18
-            return f.parse( dateString );
-        } catch ( ParseException e ) {
-            try {
-                /*
-                 * Another format we see in GPR files ... 2008:11:27 10:27:42
-                 */
-                DateFormat f = new SimpleDateFormat( "yyyy:MM:dd HH:mm:ss", Locale.ENGLISH ); // 2005/11/09 11:36:27, 2006/04/07
-                // 14:18:18
-                return f.parse( dateString );
-            } catch ( ParseException e1 ) {
-                throw new RuntimeException( e1 );
-            }
-
-        }
-    }
-
-    /**
-     * @param string ISO 8601 date time in WSTRING format based on Universal Time Clock UTC (UTC is also known as GMT, or Greenwich
-     *               Mean Time) E.g. "2005-11-23T13:45:53Z"
-     * @return date
-     */
-    protected Date parseISO8601( String string ) {
-        try {
-            Calendar f;
-            f = javax.xml.bind.DatatypeConverter.parseDateTime( string );
-            return f.getTime();
-        } catch ( Exception e ) {
-            return null;
-        }
-
-    }
-
-    /**
-     * @param string E.g. "Mon Jun 17 21:26:34 CST 2002", but line has to have Date at start (possibly white-space padded) Shows up in
-     *               Imagene files.
-     * @return date
-     */
-    protected Date parseLongFormat( String string ) {
-        try {
-            DateFormat f = new SimpleDateFormat( "EEE MMM dd HH:mm:ss zzz yyyy", Locale.ENGLISH );
-
-            Pattern regex = Pattern.compile( BaseScanDateExtractor.LONG_FORMAT_REGEX );
-
-            Matcher matcher = regex.matcher( string );
-            if ( matcher.matches() ) {
-                String tok = matcher.group( 1 );
-                return f.parse( tok );
-            }
-
-            return null;
-        } catch ( ParseException e ) {
-            throw new RuntimeException( e );
-        }
-    }
-
-    /**
-     * @param string Parse a common format, "MM[/-]dd[/-]yy hh:mm:ss", found for example in the "DatHeader" line from a CEL file and
-     *               extract the date found there.
-     * @return date
-     */
-    protected Date parseStandardFormat( String string ) {
-
-        try {
-            DateFormat f = new SimpleDateFormat( "MM/dd/yy HH:mm:ss", Locale.ENGLISH );
-
-            Pattern regex = Pattern.compile( BaseScanDateExtractor.STANDARD_FORMAT_REGEX );
-
-            Matcher matcher = regex.matcher( string );
-            if ( matcher.matches() ) {
-                String tok = matcher.group( 1 );
-                return f.parse( tok );
-            }
-
-            /*
-             * For some reason, it is common to get things like "08/26/ 3 12:30:45" - I infer that is supposed to be a
-             * 03.
-             */
-            Pattern regex2 = Pattern.compile( BaseScanDateExtractor.STANDARD_FORMAT_REGEX_2 );
-            matcher = regex2.matcher( string );
-            if ( matcher.matches() ) {
-                String tok = matcher.group( 1 );
-                tok = tok.replaceFirst( "\\s", "0" );
-                Date d = f.parse( tok );
-                BaseScanDateExtractor.log
-                        .warn( "Year was partly missing from date line: " + string + ", inferred " + d );
-                return d;
-            }
-
-            return null;
-        } catch ( ParseException e ) {
-            throw new RuntimeException( e );
-        }
-
-    }
-
-}
+/*
+ * The Gemma project
+ *
+ * Copyright (c) 2011 University of British Columbia
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *       http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package ubic.gemma.core.analysis.preprocess.batcheffects;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.Locale;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * @author paul
+ */
+@SuppressWarnings("WeakerAccess") // Possibly accessed via CLI tools
+public abstract class BaseScanDateExtractor implements ScanDateExtractor {
+
+    protected static final String GENEPIX_DATETIME_HEADER_REGEXP = "\"?DateTime=.*";
+    private static final String STANDARD_FORMAT_REGEX_2 = ".+?([0-9]{2}[/-][0-9]{2}[/-]\\s[0-9]\\s[0-9]{2}:[0-9]{2}:[0-9]{2}).+";
+    private static final String STANDARD_FORMAT_REGEX = ".+?([0-9]{2}[/-][0-9]{2}[/-][0-9]{2}\\s[0-9]{2}:[0-9]{2}:[0-9]{2}).+";
+    private static final String LONG_FORMAT_REGEX = "\\s*Date\\s*(.+)";
+    private static final Log log = LogFactory.getLog( BaseScanDateExtractor.class );
+
+    /**
+     * This method should be generic for GenePix/GPR/ATR file formats. Has DateType at the top formatted with quotes:
+     * "DateTime=2005/11/09 11:36:27". Example GSE15739
+     * For more information see <a href='http://mdc.custhelp.com/app/answers/detail/a_id/18886'>here</a>.
+     *
+     * @param reader the reader
+     * @return date
+     * @throws IOException when there was a read error
+     */
+    protected Date extractGenePix( BufferedReader reader ) throws IOException {
+        String line;
+        // GPR/ATF file. Read a few lines to find the datetime (the header tells us how long the header is, but
+        // this is probably okay)
+        Date d = null;
+        while ( ( line = reader.readLine() ) != null ) {
+
+            if ( line.matches( BaseScanDateExtractor.GENEPIX_DATETIME_HEADER_REGEXP ) ) {
+                d = this.parseGenePixDateTime( line );
+                break;
+            }
+        }
+
+        if ( d == null ) {
+            throw new IllegalStateException( "Failed to find the 'DateTime' line" );
+        }
+        reader.close();
+        return d;
+    }
+
+    /**
+     * @param line like "DateTime=2005/11/09 11:36:27" (with the quotes) possibly with trailing whitespace.
+     * @return date
+     */
+    protected Date parseGenePixDateTime( String line ) {
+        String dateString = line.trim().replaceAll( "\"", "" ).replaceFirst( "DateTime=", "" );
+        try {
+
+            DateFormat f = new SimpleDateFormat( "yyyy/MM/dd HH:mm:ss", Locale.ENGLISH ); // 2005/11/09 11:36:27, 2006/04/07 14:18:18
+            return f.parse( dateString );
+        } catch ( ParseException e ) {
+            try {
+                /*
+                 * Another format we see in GPR files ... 2008:11:27 10:27:42
+                 */
+                DateFormat f = new SimpleDateFormat( "yyyy:MM:dd HH:mm:ss", Locale.ENGLISH ); // 2005/11/09 11:36:27, 2006/04/07
+                // 14:18:18
+                return f.parse( dateString );
+            } catch ( ParseException e1 ) {
+                throw new RuntimeException( e1 );
+            }
+
+        }
+    }
+
+    /**
+     * @param string ISO 8601 date time in WSTRING format based on Universal Time Clock UTC (UTC is also known as GMT, or Greenwich
+     *               Mean Time) E.g. "2005-11-23T13:45:53Z"
+     * @return date
+     */
+    protected Date parseISO8601( String string ) {
+        try {
+            Calendar f;
+            f = javax.xml.bind.DatatypeConverter.parseDateTime( string );
+            return f.getTime();
+        } catch ( Exception e ) {
+            return null;
+        }
+
+    }
+
+    /**
+     * @param string E.g. "Mon Jun 17 21:26:34 CST 2002", but line has to have Date at start (possibly white-space padded) Shows up in
+     *               Imagene files.
+     * @return date
+     */
+    protected Date parseLongFormat( String string ) {
+        try {
+            DateFormat f = new SimpleDateFormat( "EEE MMM dd HH:mm:ss zzz yyyy", Locale.ENGLISH );
+
+            Pattern regex = Pattern.compile( BaseScanDateExtractor.LONG_FORMAT_REGEX );
+
+            Matcher matcher = regex.matcher( string );
+            if ( matcher.matches() ) {
+                String tok = matcher.group( 1 );
+                return f.parse( tok );
+            }
+
+            return null;
+        } catch ( ParseException e ) {
+            throw new RuntimeException( e );
+        }
+    }
+
+    /**
+     * @param string Parse a common format, "MM[/-]dd[/-]yy hh:mm:ss", found for example in the "DatHeader" line from a CEL file and
+     *               extract the date found there.
+     * @return date
+     */
+    protected Date parseStandardFormat( String string ) {
+
+        try {
+            DateFormat f = new SimpleDateFormat( "MM/dd/yy HH:mm:ss", Locale.ENGLISH );
+
+            Pattern regex = Pattern.compile( BaseScanDateExtractor.STANDARD_FORMAT_REGEX );
+
+            Matcher matcher = regex.matcher( string );
+            if ( matcher.matches() ) {
+                String tok = matcher.group( 1 );
+                return f.parse( tok );
+            }
+
+            /*
+             * For some reason, it is common to get things like "08/26/ 3 12:30:45" - I infer that is supposed to be a
+             * 03.
+             */
+            Pattern regex2 = Pattern.compile( BaseScanDateExtractor.STANDARD_FORMAT_REGEX_2 );
+            matcher = regex2.matcher( string );
+            if ( matcher.matches() ) {
+                String tok = matcher.group( 1 );
+                tok = tok.replaceFirst( "\\s", "0" );
+                Date d = f.parse( tok );
+                BaseScanDateExtractor.log
+                        .warn( "Year was partly missing from date line: " + string + ", inferred " + d );
+                return d;
+            }
+
+            return null;
+        } catch ( ParseException e ) {
+            throw new RuntimeException( e );
+        }
+
+    }
+
+}

gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/batcheffects/BaseScanDateExtractor.java

@@ -19,7 +19,7 @@ public class ExpressionExperimentFilterConfig implements Serializable {
     public static final double DEFAULT_LOW_EXPRESSION_CUT = 0.2;
     public static final double DEFAULT_LOW_VARIANCE_CUT = LowVarianceFilter.DEFAULT_LOW_VARIANCE_CUT;
     public static final double DEFAULT_MIN_PRESENT_FRACTION = RepetitiveValuesFilter.DEFAULT_MINIMUM_FRACTION_OF_UNIQUE_VALUES;
-    public static final int DEFAULT_MIN_PRESENT_COUNT = 7;
+    public static final int DEFAULT_MIN_PRESENT_COUNT = 4;
 
     /**
      * Mask outliers in the data by replacing the affected columns with {@link Double#NaN}.

gemma-core/src/main/java/ubic/gemma/core/analysis/preprocess/filter/ExpressionExperimentFilterConfig.java

@@ -1 +1 @@
-sample_id	cell_id	category	category_uri	category_id	value	value_uri
+sample_id	cell_id	category	category_uri	category_id	value	value_uri