diff --git a/.idea/compiler.xml b/.idea/compiler.xml deleted file mode 100644 index 96cc43e..0000000 --- a/.idea/compiler.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml deleted file mode 100644 index e7bedf3..0000000 --- a/.idea/copyright/profiles_settings.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - \ No newline at end of file diff --git a/.idea/libraries/lib.xml b/.idea/libraries/lib.xml deleted file mode 100644 index e71c7de..0000000 --- a/.idea/libraries/lib.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml deleted file mode 100644 index acb45ed..0000000 --- a/.idea/misc.xml +++ /dev/null @@ -1,73 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.8 - - - - - - - - \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml deleted file mode 100644 index 4bdd032..0000000 --- a/.idea/modules.xml +++ /dev/null @@ -1,8 +0,0 @@ - - - - - - - - \ No newline at end of file diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml deleted file mode 100644 index e96534f..0000000 --- a/.idea/uiDesigner.xml +++ /dev/null @@ -1,124 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml deleted file mode 100644 index 35eb1dd..0000000 --- a/.idea/vcs.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file diff --git a/.idea/workspace.xml b/.idea/workspace.xml deleted file mode 100644 index ff60b59..0000000 --- a/.idea/workspace.xml +++ /dev/null @@ -1,1154 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1491333853242 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - file://$PROJECT_DIR$/test/characterize/CharacterizerTest.java - 199 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/karyotyper.iml b/karyotyper.iml deleted file mode 100644 index 076a646..0000000 --- a/karyotyper.iml +++ /dev/null @@ -1,33 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/color/ISOClineColor.java b/src/Color/ISOClineColor.java similarity index 100% rename from src/color/ISOClineColor.java rename to src/Color/ISOClineColor.java diff --git a/src/color/PixelColor.java b/src/Color/PixelColor.java similarity index 100% rename from src/color/PixelColor.java rename to src/Color/PixelColor.java diff --git a/src/testing/TestShape.java b/src/testing/TestShape.java index 9a4b725..19f7257 100644 --- a/src/testing/TestShape.java +++ b/src/testing/TestShape.java @@ -1,68 +1,68 @@ -package testing; - -import runner.ImageQueue; -import chromosome.ChromosomeCluster; -import chromosome.GeneticSlideImage; -import extraction.Extractor; - -public class TestShape { - private static GeneticSlideImage image = null; - private static ChromosomeCluster cluster = null; - - /** - * @param args - */ - public static void main(String[] args) { - String filename; - ImageQueue images = new ImageQueue(); - // put new images in the queue and return the next image from the folder - // args - filename = images.getNextFile(args[0]); - // create a slideImage from the filename - GeneticSlideImage image = new GeneticSlideImage(filename); - Extractor extractor = new Extractor(); - if (filename != null) { - // extract the background from the image - int shapeNum = extractor.removeBackground(image); - // extract the clusters from the image - shapeNum = extractor.findClusters(image); - // pass on the list of clusters - ChromosomeCluster testCluster = extractor.getClusterList().get(0); - // print out the first cluster in the list - extractor.getClusterList().get(0).clusterOut(); - } - } - - /** - * Returns the chromosome cluster object from an image. - * - * @param filename - * File containing cluster - * @return The chromosome cluster object - */ - public static ChromosomeCluster getCluster(String filename) { - image = new GeneticSlideImage(filename); - Extractor extractor = new Extractor(); - ChromosomeCluster testCluster = null; - if (filename != null) { - // extract the background from the image - int shapeNum = extractor.removeBackground(image); - // extract the clusters from the image - shapeNum = extractor.findClusters(image); - // pass on the list of clusters - testCluster = extractor.getClusterList().get(0); - // print out the first cluster in the list - extractor.getClusterList().get(0).clusterOut(); - } - return testCluster; - } - - public static GeneticSlideImage getGeneticSlideImage() { - return image; - } - - public static ChromosomeCluster getCluster() { - return cluster; - } - -} +package testing; + +import runner.ImageQueue; +import chromosome.ChromosomeCluster; +import chromosome.GeneticSlideImage; +import extraction.Extractor; + +public class TestShape { + private static GeneticSlideImage image = null; + private static ChromosomeCluster cluster = null; + + /** + * @param args + */ + public static void main(String[] args) { + String filename; + ImageQueue images = new ImageQueue(); + // put new images in the queue and return the next image from the folder + // args + filename = images.getNextFile(args[0]); + // create a slideImage from the filename + GeneticSlideImage image = new GeneticSlideImage(filename); + Extractor extractor = new Extractor(); + if (filename != null) { + // extract the background from the image + int shapeNum = extractor.removeBackground(image); + // extract the clusters from the image + shapeNum = extractor.findClusters(image); + // pass on the list of clusters + ChromosomeCluster testCluster = extractor.getClusterList().get(0); + // print out the first cluster in the list + extractor.getClusterList().get(0).clusterOut(); + } + } + + /** + * Returns the chromosome cluster object from an image. + * + * @param filename + * File containing cluster + * @return The chromosome cluster object + */ + public static ChromosomeCluster getCluster(String filename) { + image = new GeneticSlideImage(filename); + Extractor extractor = new Extractor(); + ChromosomeCluster testCluster = null; + if (filename != null) { + // extract the background from the image + int shapeNum = extractor.removeBackground(image); + // extract the clusters from the image + shapeNum = extractor.findClusters(image); + // pass on the list of clusters + testCluster = extractor.getClusterList().get(0); + // print out the first cluster in the list + extractor.getClusterList().get(0).clusterOut(); + } + return testCluster; + } + + public static GeneticSlideImage getGeneticSlideImage() { + return image; + } + + public static ChromosomeCluster getCluster() { + return cluster; + } + +}