Merge pull request #22 from BackofenLab/develop

v2.0.3

.gitignore

@@ -12,3 +12,4 @@
 hs_err_pid*
 /bin
 /versions
+/gleice

Changelog.txt

@@ -1,3 +1,24 @@
+
+version 2.0.3
+
+180927 MR :
+	* R/mica-functions.R :
+	  * interpolateCurve() :
+	    * bugfix interval length formula
+
+180927 MR :
+	* controller/MicaR :
+	  * getAlignedX() :
+	  * getAlignedSlope() :
+	  * getConsensusX() :
+	  * getConsensusY() :
+	    + dedicated exception handling
+	* view/ViewCsvExpSettings : 
+	  * initForm() :
+	    * default height increased to 190 (was 150) to avoid layouting issues
+	      (thanks to Alexander Mattheis, solves PR #21)
+
+version 2.0.2
 
 180212 MR :
 	* view/View* : 

R/mica-functions.R

@@ -27,13 +27,13 @@ initMica <- function( micaJavaPath ) {
 
 	# check if all-in-one mica.jar available
 	allInOneJarAvailable = FALSE;
-	if (sum(file.access(paste(micaJavaPath ,"\\mica.jar",sep=""),4)) == 0 )  {
+	if (sum(file.access(paste(micaJavaPath, .Platform$file.sep, "mica.jar",sep=""),4)) == 0 )  {
 		allInOneJarAvailable = TRUE;
 	}
 	# check if dependencies are available
 	depJars = c("commons-lang3-3.4.jar","commons-math3-3.6.1.jar","java-hamcrest-2.0.0.0.jar");
 	for( depJar in depJars ) {
-		if (sum(file.access(paste(micaJavaPath,depJar,sep="\\"),4)) != 0 ) stop(paste("given micaJavaPath='",micaJavaPath,"' does not contain needed jar file '",depJar,"'",sep=""));
+		if (sum(file.access(paste(micaJavaPath,depJar,sep=.Platform$file.sep),4)) != 0 ) stop(paste("given micaJavaPath='",micaJavaPath,"' does not contain needed jar file '",depJar,"'",sep=""));
 	}
 
 	# initialize java interface
@@ -44,12 +44,12 @@ initMica <- function( micaJavaPath ) {
 
 	# extend classpath accordingly
 	if (allInOneJarAvailable) {
-		rJava::.jaddClassPath(paste(micaJavaPath ,"\\mica.jar",sep=""));
+		rJava::.jaddClassPath(paste(micaJavaPath,.Platform$file.sep,"mica.jar",sep=""));
 	} else {
 		rJava::.jaddClassPath(micaJavaPath)
 	}
 	for( depJar in depJars ) {
-		rJava::.jaddClassPath(paste(micaJavaPath,depJar,sep="\\"));
+		rJava::.jaddClassPath(paste(micaJavaPath,depJar,sep=.Platform$file.sep));
 	}
 
 	micaSetup$wasInitialized <<- TRUE;
@@ -273,7 +273,7 @@ interpolateCurve <- function( x, y, samples ) {
 	if (length(y)<3) stop("min length of y is 3");
 
 	# create x data to be interpolated
-	xNew <- x[1] + ((x[length(x)-x[1]])*((0:(samples-1))/(samples-1)));
+	xNew <- x[1] + ((x[length(x)]-x[1])*((0:(samples-1))/(samples-1)));
 
 	# create curve object
 	jCurve <- rJava::.jnew("de/uni_freiburg/bioinf/mica/algorithm/Curve","newCurve", x, y );

src/de/uni_freiburg/bioinf/mica/controller/MicaController.java

@@ -8,7 +8,7 @@ public interface MicaController {
 	/**
 	 * Version information
 	 */
-	public static final String version = "2.0.1";
+	public static final String version = "2.0.3";
 
 	/**
 	 * To describe on what basis the distance function is to be computed

src/de/uni_freiburg/bioinf/mica/controller/MicaR.java

@@ -284,9 +284,10 @@ public double[] getCurveSlope( int curveIdx ) {
 
 		if (isAligned()) {
 			return originalCurves.get(curveIdx).getCurveOriginal().getSlope();
+		} else {
+			// emergency handling
+			throw new IllegalStateException("no alignment available yet, did you call 'align' yet?");
 		}
-		// emergency handling
-		return new double[0];
 	}
 
 	/**
@@ -308,9 +309,12 @@ public double[] getAlignedSlope( int curveIdx ) {
 					return d.getCurve().getSlope();
 				}
 			}
+			// emergency handling
+			throw new RuntimeException("could not find the aligned data for curve"+String.valueOf(curveIdx));
+		} else {
+			// emergency handling
+			throw new IllegalStateException("no alignment available yet, did you call 'align' yet?");
 		}
-		// emergency handling
-		return new double[0];
 	}
 
 
@@ -333,9 +337,12 @@ public double[] getAlignedX( int curveIdx ) {
 					return d.getCurve().getX();
 				}
 			}
+			// emergency handling
+			throw new RuntimeException("could not find the aligned data for curve"+String.valueOf(curveIdx));
+		} else {
+			// emergency handling
+			throw new IllegalStateException("no alignment available yet, did you call 'align' yet?");
 		}
-		// emergency handling
-		return new double[0];
 	}
 
 	/**
@@ -353,9 +360,10 @@ public boolean isAligned() {
 	public double[] getConsensusX() {
 		if (isAligned()) {
 			return alignment.consensus.getCurve().getX();
+		} else {
+			// emergency handling
+			throw new IllegalStateException("no alignment available yet, did you call 'align' yet?");
 		}
-		// emergency handling
-		return new double[0];
 	}
 
 	/**
@@ -365,9 +373,10 @@ public double[] getConsensusX() {
 	public double[] getConsensusY() {
 		if (isAligned()) {
 			return alignment.consensus.getCurve().getY();
+		} else {
+			// emergency handling
+			throw new IllegalStateException("no alignment available yet, did you call 'align' yet?");
 		}
-		// emergency handling
-		return new double[0];
 	}
 
 	/**

src/de/uni_freiburg/bioinf/mica/view/ViewCsvExpSettings.java

@@ -242,7 +242,8 @@ private void initForm() {
 
 		// Set the properties of this frame.
 		this.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
-		this.setMinimumSize(new Dimension(400, 150));
+		this.setMinimumSize(new Dimension(400, 190));
+		this.setResizable(false);
 		this.setLocationRelativeTo(null);
 
 		// Add listener if the user closes the window with the [x]